To execute picard run: java -jar $EBROOTPICARD/picard.jar
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
	LANGUAGE = (unset),
	LC_ALL = (unset),
	LC_CTYPE = "UTF-8",
	LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
 [ Wed Dec 25 11:22:37 2019 ] processBAM::processBAM(..): Start graph gap analysis.
 [ Wed Dec 25 11:22:41 2019 ] processBAM::processBAM(..) graph gap analysis: have 3494 graph gap stretches; criterion length >= 3
/tarafs/biobank/data/modules/.local/easybuild/software/BWA/0.7.17-foss-2018b/bin/bwa mem -t40 -M -a /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_1.fastq /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_2.fastq | /tarafs/biobank/data/modules/.local/easybuild/software/SAMtools/1.9-foss-2018b/bin/samtools view -@ 39 -Sb - > /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/remapped_with_a.bam.unsorted
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 810188 sequences (81828988 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 3020, 0, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (269, 314, 358)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (91, 536)
[M::mem_pestat] mean and std.dev: (311.70, 72.46)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 625)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 810188 reads in 261.192 CPU sec, 6.971 real sec
[main] Version: 0.7.17-r1188
[main] CMD: /tarafs/biobank/data/modules/.local/easybuild/software/BWA/0.7.17-foss-2018b/bin/bwa mem -t40 -M -a /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_1.fastq /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_2.fastq
[main] Real time: 13.357 sec; CPU: 265.968 sec
/tarafs/biobank/data/modules/.local/easybuild/software/SAMtools/1.9-foss-2018b/bin/samtools sort -@ 40 -o /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/remapped_with_a.bam /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/remapped_with_a.bam.unsorted
[bam_sort_core] merging from 0 files and 40 in-memory blocks...
/tarafs/biobank/data/modules/.local/easybuild/software/SAMtools/1.9-foss-2018b/bin/samtools index /tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/remapped_with_a.bam
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Warning: Can't G-translate: B*07:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: B*07:44; have only things like A*01:01:01:01Warning: Can't G-translate: B*07:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: B*07:44; have only things like A*01:01:01:01Warning: Can't G-translate: C*01:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: C*01:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: DQA1*05:03; have only things like A*01:01:01:01Warning: Can't G-translate: DQA1*05:06; have only things like A*01:01:01:01Warning: Can't G-translate: DQB1*02:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: DQB1*02:02:01; have only things like A*01:01:01:01Warning: Can't G-translate: DPA1*02:01:01; have only things like A*01:01:01:01Warning: Can't G-translate: DPA1*02:01:08; have only things like A*01:01:01:01Warning: Can't G-translate: DPB1*126:01; have only things like A*01:01:01:01Warning: Can't G-translate: DPB1*14:01:01; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:01; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:02; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:03; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:04; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:01; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:02; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:03; have only things like A*01:01:01:01Warning: Can't G-translate: F*01:01:03:04; have only things like A*01:01:01:01Warning: Can't G-translate: G*01:08; have only things like A*01:01:01:01