---- Checking for available reference files ---- Thu May 4 14:13:33 EDT 2023 timestamp: 1683224013 ---- Reference files not found - Files will be downloaded ---- Thu May 4 14:13:33 EDT 2023 timestamp: 1683224013 ---- Starting Mouse Cancer Genome Analysis ---- Starting pipeline using these settings: Fri May 5 05:38:34 EDT 2023 timestamp: 1683279514 Running sample named MoCaSeq_Test Running in MS-mode Using /opt/MoCaSeq/test/Mouse.Normal.R1.fastq.gz and /opt/MoCaSeq/test/Mouse.Normal.R2.fastq.gz for normal fastqs Using /opt/MoCaSeq/test/Mouse.Tumor.R1.fastq.gz and /opt/MoCaSeq/test/Mouse.Tumor.R2.fastq.gz for tumor fastqs Assuming that reads are from Mouse Assuming that experiment is WES Reading configuration file from /opt/MoCaSeq/config.sh Setting location of repository to /opt/MoCaSeq/repository Setting location of genome to /var/pipeline/ref/GRCm38.p6 Setting location for temporary files to /var/pipeline/temp Assuming none-artefacts for SNV-calling all is setting for filtering of SNV calls Quality scores are assumed as Using GATK v4.1.7.0 Will run Mutect2 Starting workflow using 4 CPU-threads and 8 GB of RAM ---- Creating directories ---- Fri May 5 05:38:34 EDT 2023 timestamp: 1683279514 ---- Copying repository ---- Fri May 5 05:38:34 EDT 2023 timestamp: 1683279514 ---- Copying raw data ---- Fri May 5 05:38:35 EDT 2023 timestamp: 1683279515 ---- Calculating md5-sums ---- Fri May 5 05:38:38 EDT 2023 timestamp: 1683279518 ---- Running FastQC before trimming ---- Fri May 5 05:38:38 EDT 2023 timestamp: 1683279518 Started analysis of MoCaSeq_Test.Tumor.R1.fastq.gz Started analysis of MoCaSeq_Test.Normal.R1.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R2.fastq.gzStarted analysis of MoCaSeq_Test.Normal.R2.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 25% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 25% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 30% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 30% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 35% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 35% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 40% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 40% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R2.fastq.gz Approx 100% complete for MoCaSeq_Test.Tumor.R1.fastq.gz Approx 100% complete for MoCaSeq_Test.Normal.R1.fastq.gz Approx 100% complete for MoCaSeq_Test.Normal.R2.fastq.gz Approx 100% complete for MoCaSeq_Test.Tumor.R2.fastq.gz ---- Trimming reads ---- Fri May 5 05:38:52 EDT 2023 timestamp: 1683279532 TrimmomaticPE: Started with arguments: -threads 4 -phred33 MoCaSeq_Test/fastq/MoCaSeq_Test.Normal.R1.fastq.gz MoCaSeq_Test/fastq/MoCaSeq_Test.Normal.R2.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R1.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R1.not_passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R2.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R2.not_passed.fastq.gz LEADING:25 TRAILING:25 MINLEN:50 SLIDINGWINDOW:10:25 ILLUMINACLIP:/opt/trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 TrimmomaticPE: Started with arguments: -threads 4 -phred33 MoCaSeq_Test/fastq/MoCaSeq_Test.Tumor.R1.fastq.gz MoCaSeq_Test/fastq/MoCaSeq_Test.Tumor.R2.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R1.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R1.not_passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R2.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R2.not_passed.fastq.gz LEADING:25 TRAILING:25 MINLEN:50 SLIDINGWINDOW:10:25 ILLUMINACLIP:/opt/trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequencesUsing Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 1000000 Both Surviving: 969667 (96.97%) Forward Only Surviving: 29456 (2.95%) Reverse Only Surviving: 499 (0.05%) Dropped: 378 (0.04%) Input Read Pairs: 1000000 Both Surviving: 972646 (97.26%) Forward Only Surviving: 26622 (2.66%) Reverse Only Surviving: 497 (0.05%) Dropped: 235 (0.02%) TrimmomaticPE: Completed successfully TrimmomaticPE: Completed successfully ---- Running FastQC after trimming ---- Fri May 5 05:39:16 EDT 2023 timestamp: 1683279556 Started analysis of MoCaSeq_Test.Normal.R1.passed.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R1.passed.fastq.gz Started analysis of MoCaSeq_Test.Normal.R2.passed.fastq.gz Started analysis of MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 5% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 10% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 15% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 20% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 20% complete for 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MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 45% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 50% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 55% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 60% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 65% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 70% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 75% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 80% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 85% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 90% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R1.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R1.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Tumor.R2.passed.fastq.gz Approx 95% complete for MoCaSeq_Test.Normal.R2.passed.fastq.gz ---- Removing fastq files ---- Fri May 5 05:39:28 EDT 2023 timestamp: 1683279568 ---- Mapping trimmed reads ---- Fri May 5 05:39:28 EDT 2023 timestamp: 1683279568 09:39:28.847 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:39:28 UTC 2023] CleanSam --INPUT /dev/stdin --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.bam --VALIDATION_STRINGENCY LENIENT --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:39:28 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [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: (141, 177, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 396) [M::mem_pestat] mean and std.dev: (188.10, 61.13) [M::mem_pestat] low and high boundaries for proper pairs: (1, 481) [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_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: (142, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.29, 60.41) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (141, 177, 227) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 399) [M::mem_pestat] mean and std.dev: (188.60, 61.32) [M::mem_pestat] low and high boundaries for proper pairs: (1, 485) [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_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: (142, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.61, 60.66) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (143, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 392) [M::mem_pestat] mean and std.dev: (188.41, 59.97) [M::mem_pestat] low and high boundaries for proper pairs: (1, 475) [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_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: (142, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.58, 60.71) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (141, 177, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 396) [M::mem_pestat] mean and std.dev: (188.23, 60.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 481) [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_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: (141, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 396) [M::mem_pestat] mean and std.dev: (188.84, 60.95) [M::mem_pestat] low and high boundaries for proper pairs: (1, 481) [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_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: (142, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.21, 60.28) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (142, 177, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.22, 60.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs INFO 2023-05-05 09:40:24 CleanSam Processed 1,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 38s. Last read position: 14:42,436,963 [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: (142, 179, 227) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397) [M::mem_pestat] mean and std.dev: (188.86, 60.76) [M::mem_pestat] low and high boundaries for proper pairs: (1, 482) [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_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: (142, 178, 227) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397) [M::mem_pestat] mean and std.dev: (189.01, 61.29) [M::mem_pestat] low and high boundaries for proper pairs: (1, 482) [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_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: (142, 179, 227) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397) [M::mem_pestat] mean and std.dev: (189.36, 61.12) [M::mem_pestat] low and high boundaries for proper pairs: (1, 482) [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_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: (142, 177, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.38, 60.99) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (142, 178, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (188.20, 60.41) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (142, 179, 228) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 400) [M::mem_pestat] mean and std.dev: (189.45, 61.36) [M::mem_pestat] low and high boundaries for proper pairs: (1, 486) [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_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: (142, 177, 226) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394) [M::mem_pestat] mean and std.dev: (187.96, 60.51) [M::mem_pestat] low and high boundaries for proper pairs: (1, 478) [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_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: (142, 178, 227) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397) [M::mem_pestat] mean and std.dev: (188.97, 61.20) [M::mem_pestat] low and high boundaries for proper pairs: (1, 482) [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_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: (142, 179, 229) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 403) [M::mem_pestat] mean and std.dev: (189.62, 61.63) [M::mem_pestat] low and high boundaries for proper pairs: (1, 490) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -t 4 -Y -K 10000000 -v 1 /var/pipeline/ref/GRCm38.p6/bwa_index/GRCm38.p6 /var/pipeline/temp/MoCaSeq_Test.Tumor.R1.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Tumor.R2.passed.fastq.gz [main] Real time: 93.776 sec; CPU: 318.509 sec [Fri May 05 09:41:02 UTC 2023] picard.sam.CleanSam done. Elapsed time: 1.55 minutes. Runtime.totalMemory()=1823997952 09:41:02.667 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:41:02 UTC 2023] CleanSam --INPUT /dev/stdin --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.bam --VALIDATION_STRINGENCY LENIENT --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:41:02 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.44, 51.65) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 163, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (172.58, 51.38) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 165, 206) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 350) [M::mem_pestat] mean and std.dev: (173.58, 51.45) [M::mem_pestat] low and high boundaries for proper pairs: (1, 422) [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_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: (133, 163, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 349) [M::mem_pestat] mean and std.dev: (172.80, 51.33) [M::mem_pestat] low and high boundaries for proper pairs: (1, 421) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.04, 51.63) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (172.86, 51.01) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (172.86, 50.94) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.18, 51.53) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 204) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 344) [M::mem_pestat] mean and std.dev: (172.58, 50.78) [M::mem_pestat] low and high boundaries for proper pairs: (1, 414) [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_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: (134, 165, 206) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 350) [M::mem_pestat] mean and std.dev: (173.36, 51.93) [M::mem_pestat] low and high boundaries for proper pairs: (1, 422) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs INFO 2023-05-05 09:41:45 CleanSam Processed 1,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 36s. Last read position: 15:99,711,033 [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: (134, 164, 206) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 350) [M::mem_pestat] mean and std.dev: (173.63, 51.66) [M::mem_pestat] low and high boundaries for proper pairs: (1, 422) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (172.79, 51.23) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (133, 164, 206) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 352) [M::mem_pestat] mean and std.dev: (173.33, 51.96) [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.15, 51.44) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.37, 51.55) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.17, 51.67) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 163, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (172.81, 51.37) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (134, 165, 206) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 350) [M::mem_pestat] mean and std.dev: (173.61, 51.48) [M::mem_pestat] low and high boundaries for proper pairs: (1, 422) [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_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: (134, 164, 205) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 347) [M::mem_pestat] mean and std.dev: (173.19, 51.65) [M::mem_pestat] low and high boundaries for proper pairs: (1, 418) [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_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: (133, 165, 204) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 346) [M::mem_pestat] mean and std.dev: (171.93, 49.97) [M::mem_pestat] low and high boundaries for proper pairs: (1, 417) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -t 4 -Y -K 10000000 -v 1 /var/pipeline/ref/GRCm38.p6/bwa_index/GRCm38.p6 /var/pipeline/temp/MoCaSeq_Test.Normal.R1.passed.fastq.gz /var/pipeline/temp/MoCaSeq_Test.Normal.R2.passed.fastq.gz [main] Real time: 79.784 sec; CPU: 308.304 sec [Fri May 05 09:42:21 UTC 2023] picard.sam.CleanSam done. Elapsed time: 1.32 minutes. Runtime.totalMemory()=1824522240 ---- Postprocessing I (Sorting, fixing read groups and marking duplicates) ---- Fri May 5 05:42:21 EDT 2023 timestamp: 1683279741 sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4) sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4) 09:42:30.557 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 09:42:30.561 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:42:30 UTC 2023] AddOrReplaceReadGroups --INPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.sorted.bam --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Normal.cleaned.sorted.readgroups.bam --RGID 1 --RGLB Lib1 --RGPL ILLUMINA --RGPU Run1 --RGSM Normal --MAX_RECORDS_IN_RAM 2000000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:42:30 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:42:30 UTC 2023] AddOrReplaceReadGroups --INPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.bam --OUTPUT /var/pipeline/temp/MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.bam --RGID 1 --RGLB Lib1 --RGPL ILLUMINA --RGPU Run1 --RGSM Tumor --MAX_RECORDS_IN_RAM 2000000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:42:30 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT INFO 2023-05-05 09:42:30 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=Lib1 SM=Normal INFO 2023-05-05 09:42:30 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=Lib1 SM=Tumor INFO 2023-05-05 09:42:43 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: 9:29,069,301 INFO 2023-05-05 09:42:43 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: 9:55,858,046 [Fri May 05 09:42:55 UTC 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.42 minutes. Runtime.totalMemory()=1932001280 sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4) finding positions of the duplicate reads in the file... [Fri May 05 09:42:55 UTC 2023] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.42 minutes. Runtime.totalMemory()=1932001280 sambamba 0.7.0 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4) finding positions of the duplicate reads in the file... sorted 946482 end pairs and 16357 single ends (among them 0 unmatched pairs) collecting indices of duplicate reads... sorted 937409 end pairs and 21665 single ends (among them 0 unmatched pairs) collecting indices of duplicate reads... done in 233 ms found 135599 duplicates collected list of positions in 0 min 12 sec done in 227 ms found 136762 duplicates marking duplicates... collected list of positions in 0 min 11 sec marking duplicates... collected list of positions in 0 min 20 sec collected list of positions in 0 min 20 sec ---- Postprocessing II (Base recalibration) ---- Fri May 5 05:43:16 EDT 2023 timestamp: 1683279796 09:43:20.982 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 09:43:20.982 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:43:21 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. May 05, 2023 9:43:21 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:43:21.456 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.456 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.457 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:43:21.457 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:43:21.457 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:43:21.457 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:43:21.457 INFO BaseRecalibrator - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:43:21.457 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:43:21.457 INFO BaseRecalibrator - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:43:21.457 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:43:21.457 INFO BaseRecalibrator - Start Date/Time: May 5, 2023 9:43:20 AM UTC 09:43:21.457 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.457 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.457 INFO BaseRecalibrator - Start Date/Time: May 5, 2023 9:43:20 AM UTC 09:43:21.457 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.457 INFO BaseRecalibrator - ------------------------------------------------------------ 09:43:21.458 INFO BaseRecalibrator - HTSJDK Version: 2.21.2 09:43:21.458 INFO BaseRecalibrator - Picard Version: 2.21.9 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:43:21.458 INFO BaseRecalibrator - HTSJDK Version: 2.21.2 09:43:21.458 INFO BaseRecalibrator - Picard Version: 2.21.9 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:43:21.458 INFO BaseRecalibrator - Deflater: IntelDeflater 09:43:21.458 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:43:21.458 INFO BaseRecalibrator - Inflater: IntelInflater 09:43:21.458 INFO BaseRecalibrator - Deflater: IntelDeflater 09:43:21.458 INFO BaseRecalibrator - GCS max retries/reopens: 20 09:43:21.458 INFO BaseRecalibrator - Inflater: IntelInflater 09:43:21.458 INFO BaseRecalibrator - Requester pays: disabled 09:43:21.458 INFO BaseRecalibrator - GCS max retries/reopens: 20 09:43:21.458 INFO BaseRecalibrator - Initializing engine 09:43:21.458 INFO BaseRecalibrator - Requester pays: disabled 09:43:21.458 INFO BaseRecalibrator - Initializing engine 09:43:21.770 INFO BaseRecalibrator - Shutting down engine 09:43:21.771 INFO BaseRecalibrator - Shutting down engine [May 5, 2023 9:43:21 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2080899072 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///var/pipeline/ref/GRCm38.p6/MGP.v5.snp_and_indels.exclude_wild.vcf.gz. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. [May 5, 2023 9:43:21 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2042626048 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///var/pipeline/ref/GRCm38.p6/MGP.v5.snp_and_indels.exclude_wild.vcf.gz. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Quality control I (Sequencing artifacts, multiple metrics) ---- Fri May 5 05:43:21 EDT 2023 timestamp: 1683279801 [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools idxstats: failed to open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools idxstats: failed to open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory 09:43:22.577 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:43:22 UTC 2023] CollectMultipleMetrics --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Tumor.bam.metrics --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --ASSUME_SORTED true --STOP_AFTER 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectBaseDistributionByCycle --PROGRAM CollectInsertSizeMetrics --PROGRAM MeanQualityByCycle --PROGRAM QualityScoreDistribution --INCLUDE_UNPAIRED false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:22 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT 09:43:22.599 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:43:22 UTC 2023] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:95) at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:563) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) 09:43:22.610 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 09:43:22.610 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:43:22 UTC 2023] CollectSequencingArtifactMetrics --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Normal.bam.artifacts --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --CONTEXT_SIZE 1 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:22 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:43:22 UTC 2023] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:95) at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:84) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) [Fri May 05 09:43:22 UTC 2023] CollectSequencingArtifactMetrics --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Tumor.bam.artifacts --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --CONTEXT_SIZE 1 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:22 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:43:22 UTC 2023] CollectMultipleMetrics --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Normal.bam.metrics --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --ASSUME_SORTED true --STOP_AFTER 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --PROGRAM CollectAlignmentSummaryMetrics --PROGRAM CollectBaseDistributionByCycle --PROGRAM CollectInsertSizeMetrics --PROGRAM MeanQualityByCycle --PROGRAM QualityScoreDistribution --INCLUDE_UNPAIRED false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:22 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:43:22 UTC 2023] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:95) at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:84) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) [Fri May 05 09:43:22 UTC 2023] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:95) at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:563) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) ---- Quality control II (WES- or WGS-specific metrics) ---- Fri May 5 05:43:22 EDT 2023 timestamp: 1683279802 09:43:23.338 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so 09:43:23.338 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/picard-2.20.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Fri May 05 09:43:23 UTC 2023] CollectHsMetrics --BAIT_INTERVALS /var/pipeline/ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --TARGET_INTERVALS /var/pipeline/ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Normal.bam.metrics --SAMPLE_SIZE 100000 --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:23 UTC 2023] CollectHsMetrics --BAIT_INTERVALS /var/pipeline/ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --TARGET_INTERVALS /var/pipeline/ref/GRCm38.p6/GRCm38.SureSelect_Mouse_All_Exon_V1.bed.list --INPUT MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam --OUTPUT MoCaSeq_Test/results/QC/MoCaSeq_Test.Tumor.bam.metrics --SAMPLE_SIZE 100000 --REFERENCE_SEQUENCE /var/pipeline/ref/GRCm38.p6/GRCm38.p6.fna --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Fri May 05 09:43:23 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:43:23 UTC 2023] Executing as dcook@galen64 on Linux 4.18.0-348.20.1.el8_5.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_265-8u265-b01-0ubuntu2~18.04-b01; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.20.0-SNAPSHOT [Fri May 05 09:43:23 UTC 2023] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Fri May 05 09:43:23 UTC 2023] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058354688 Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bamhtsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:405) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:392) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:116) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:116) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) ---- Summarizing quality control data ---- Fri May 5 05:43:23 EDT 2023 timestamp: 1683279803 [WARNING] multiqc : MultiQC Version v1.14 now available! [INFO ] multiqc : This is MultiQC v1.9 [INFO ] multiqc : --pdf specified. Using non-interactive HTML template. [INFO ] multiqc : Template : simple [WARNING] multiqc : You are running MultiQC with Python 2.7.17 [WARNING] multiqc : Please upgrade! MultiQC will soon drop support for Python < 3.6 [INFO ] multiqc : Searching : /home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/QC [ERROR ] multiqc : Oops! The 'somalier' MultiQC module broke... Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues If possible, please include a log file that triggers the error - the last file found was: None ============================================================ Module somalier raised an exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/multiqc/multiqc.py", line 567, in run mod = config.avail_modules[this_module].load() File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2443, in load return self.resolve() File "/usr/local/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2449, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/usr/local/lib/python2.7/dist-packages/multiqc/modules/somalier/__init__.py", line 3, in from .somalier import MultiqcModule File "/usr/local/lib/python2.7/dist-packages/multiqc/modules/somalier/somalier.py", line 698 cols_return.append('rgba({},{},{},{})'.format(*cols_rgb, alpha)) SyntaxError: only named arguments may follow *expression ============================================================ [INFO ] trimmomatic : Found 1 logs [INFO ] fastqc : Found 8 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : MoCaSeq_Test/results/QC/MoCaSeq_Test.html [INFO ] multiqc : Data : MoCaSeq_Test/results/QC/MoCaSeq_Test_data pandoc: unrecognized option `--pdf-engine=xelatex' Try pandoc --help for more information. [ERROR ] multiqc : Error creating PDF! Pandoc returned a non-zero exit code. [INFO ] multiqc : MultiQC complete ---- Matched BAM-files? ---- Fri May 5 05:43:36 EDT 2023 timestamp: 1683279816 ---- Get genotypes ---- Fri May 5 05:43:37 EDT 2023 timestamp: 1683279817 [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam: No such file or directory [warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. [warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory [mpileup] failed to open MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam: No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam": No such file or directory [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam" : No such file or directory samtools depth: Could not open "MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam": No such file or directory Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted cat: MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt: No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Genotype/MoCaSeq_Test.Genotypes.temp.CNV.txt': No such file or directory rm: cannot remove 'Rplots.pdf': No such file or directory ---- Running Manta (matched tumor-normal) ---- Fri May 5 05:43:43 EDT 2023 timestamp: 1683279823 Usage: configManta.py [options] configManta.py: error: Can't find normal sample BAM/CRAM file: '/home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam' python2: can't open file 'MoCaSeq_Test/results/Manta/runWorkflow.py': [Errno 2] No such file or directory cp: cannot stat 'MoCaSeq_Test/results/Manta/results/variants/somaticSV.vcf.gz': No such file or directory gzip: MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf.gz: No such file or directory cat: MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf: No such file or directory Failed to read from MoCaSeq_Test/results/Manta/MoCaSeq_Test.Manta.vcf.gz: unknown file type rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.man.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.one.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Tumor.Manta.vcf.gz.tbi': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.one.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Manta/MoCaSeq_Test.Normal.Manta.vcf.gz.tbi': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory -------------------- EXCEPTION -------------------- MSG: ERROR: PolyPhen not available STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168 STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121 STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:44:05 2023 Ensembl API version = 96 --------------------------------------------------- STATUS: Running VEP and writing to: MoCaSeq_Test/results/Manta/MoCaSeq_Test.Manta.vep.vcf ---- Running Strelka (matched tumor-normal) ---- Fri May 5 05:44:37 EDT 2023 timestamp: 1683279877 Usage: configureStrelkaSomaticWorkflow.py [options] configureStrelkaSomaticWorkflow.py: error: Can't find expected candidate indel vcf file: 'MoCaSeq_Test/results/Manta/results/variants/candidateSmallIndels.vcf.gz' python2: can't open file 'MoCaSeq_Test/results/Strelka/Strelka/runWorkflow.py': [Errno 2] No such file or directory ---- Strelka Postprocessing I (Indel size selection, filtering) ---- Fri May 5 05:44:37 EDT 2023 timestamp: 1683279877 gzip: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.snvs.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.indels.vcf.gz: No such file or directory cat: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.snvs.vcf: No such file or directory cat: MoCaSeq_Test/results/Strelka/Strelka/results/variants/somatic.indels.vcf: No such file or directory 09:44:39.652 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:44:39 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:44:39.828 INFO SelectVariants - ------------------------------------------------------------ 09:44:39.828 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:44:39.828 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:44:39.829 INFO SelectVariants - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:44:39.829 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:44:39.829 INFO SelectVariants - Start Date/Time: May 5, 2023 9:44:39 AM UTC 09:44:39.829 INFO SelectVariants - ------------------------------------------------------------ 09:44:39.829 INFO SelectVariants - ------------------------------------------------------------ 09:44:39.829 INFO SelectVariants - HTSJDK Version: 2.21.2 09:44:39.829 INFO SelectVariants - Picard Version: 2.21.9 09:44:39.829 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:44:39.829 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:44:39.829 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:44:39.829 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:44:39.829 INFO SelectVariants - Deflater: IntelDeflater 09:44:39.829 INFO SelectVariants - Inflater: IntelInflater 09:44:39.830 INFO SelectVariants - GCS max retries/reopens: 20 09:44:39.830 INFO SelectVariants - Requester pays: disabled 09:44:39.830 INFO SelectVariants - Initializing engine 09:44:40.087 INFO SelectVariants - Shutting down engine [May 5, 2023 9:44:40 AM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2183659520 *********************************************************************** A USER ERROR has occurred: Cannot read file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.filtered.vcf because no suitable codecs found *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Strelka Postprocessing II (Filtering out known SNV/Indel using dbSNP or the Sanger Mouse database) ---- Fri May 5 05:44:40 EDT 2023 timestamp: 1683279880 [bgzip] No such file or directory: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf tbx_index_build failed: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz" : No such file or directory Failed to open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz: No such file or directory mv: cannot stat 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.snp_removed.vcf.gz': No such file or directory gzip: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vcf.gz: No such file or directory Failed to open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.snp.postprocessed.vcf.gz: unknown file type mv: cannot stat 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.snp.postprocessed.snp_removed.vcf.gz': No such file or directory gzip: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vcf.gz: No such file or directory ---- Strelka Postprocessing III (Extracting allele frequencies) ---- Fri May 5 05:44:40 EDT 2023 timestamp: 1683279880 -------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /home/wranalab/dcook/.vep/mus_musculus not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:44:40 2023 Ensembl API version = 96 --------------------------------------------------- -------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /home/wranalab/dcook/.vep/mus_musculus not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:44:40 2023 Ensembl API version = 96 --------------------------------------------------- ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vcf ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vcf ERROR: Couldn't open input MAF: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vep.maf! ERROR: Couldn't open input MAF: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vep.maf! sed: can't read MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf: No such file or directory sed: can't read MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.maf.vcf: No such file or directory [bgzip] No such file or directory: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf [bgzip] No such file or directory: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.maf.vcf tbx_index_build failed: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf.gz tbx_index_build failed: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.maf.vcf.gz Checking the headers and starting positions of 2 files [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf.gz" : No such file or directory Failed to open: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf.gz ---- Strelka Postprocessing IV (Annotate calls) ---- Fri May 5 05:44:40 EDT 2023 timestamp: 1683279880 rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.gz.tbi': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.str.indel.postprocessed.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann1.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann2.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann3.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann4.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann5.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann6.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.ann7.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.maf.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.maf.vcf.gz.tbi': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vep.maf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vep.pairs.tsv': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.indel.vep.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.maf.vcf.gz.tbi': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vep.maf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vep.pairs.tsv': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.snp.vep.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Strelka/MoCaSeq_Test_vs_NORMAL.vcf': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory -------------------- EXCEPTION -------------------- MSG: ERROR: PolyPhen not available STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168 STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121 STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:45:00 2023 Ensembl API version = 96 --------------------------------------------------- ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.vcf awk: cannot open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Strelka/MoCaSeq_Test.Strelka.vep.maf (No such file or directory) Usage: configureStrelkaGermlineWorkflow.py [options] configureStrelkaGermlineWorkflow.py: error: Can't find input BAM/CRAM file: '/home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam' Usage: configureStrelkaGermlineWorkflow.py [options] configureStrelkaGermlineWorkflow.py: error: Can't find input BAM/CRAM file: '/home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam' ---- Running Mutect2 (matched tumor-normal) ---- Fri May 5 05:45:00 EDT 2023 timestamp: 1683279900 09:45:02.839 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:03 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:03.016 INFO Mutect2 - ------------------------------------------------------------ 09:45:03.016 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:03.016 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:03.016 INFO Mutect2 - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:03.016 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:03.016 INFO Mutect2 - Start Date/Time: May 5, 2023 9:45:02 AM UTC 09:45:03.016 INFO Mutect2 - ------------------------------------------------------------ 09:45:03.016 INFO Mutect2 - ------------------------------------------------------------ 09:45:03.017 INFO Mutect2 - HTSJDK Version: 2.21.2 09:45:03.017 INFO Mutect2 - Picard Version: 2.21.9 09:45:03.017 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:03.017 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:03.017 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:03.017 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:03.017 INFO Mutect2 - Deflater: IntelDeflater 09:45:03.017 INFO Mutect2 - Inflater: IntelInflater 09:45:03.017 INFO Mutect2 - GCS max retries/reopens: 20 09:45:03.017 INFO Mutect2 - Requester pays: disabled 09:45:03.017 INFO Mutect2 - Initializing engine 09:45:03.074 INFO Mutect2 - Shutting down engine [May 5, 2023 9:45:03 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2186280960 *********************************************************************** A USER ERROR has occurred: Couldn't read file. Error was: MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam with exception: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Mutect2 Postprocessing (matched tumor-normal) ---- Fri May 5 05:45:03 EDT 2023 timestamp: 1683279903 ---- Mutect2 Postprocessing I (OrientationFilter, Indel size selection, filtering) ---- Fri May 5 05:45:03 EDT 2023 timestamp: 1683279903 09:45:04.993 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:05 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:05.167 INFO LearnReadOrientationModel - ------------------------------------------------------------ 09:45:05.168 INFO LearnReadOrientationModel - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:05.168 INFO LearnReadOrientationModel - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:05.168 INFO LearnReadOrientationModel - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:05.168 INFO LearnReadOrientationModel - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:05.168 INFO LearnReadOrientationModel - Start Date/Time: May 5, 2023 9:45:04 AM UTC 09:45:05.168 INFO LearnReadOrientationModel - ------------------------------------------------------------ 09:45:05.168 INFO LearnReadOrientationModel - ------------------------------------------------------------ 09:45:05.169 INFO LearnReadOrientationModel - HTSJDK Version: 2.21.2 09:45:05.169 INFO LearnReadOrientationModel - Picard Version: 2.21.9 09:45:05.169 INFO LearnReadOrientationModel - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:05.169 INFO LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:05.169 INFO LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:05.169 INFO LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:05.169 INFO LearnReadOrientationModel - Deflater: IntelDeflater 09:45:05.169 INFO LearnReadOrientationModel - Inflater: IntelInflater 09:45:05.169 INFO LearnReadOrientationModel - GCS max retries/reopens: 20 09:45:05.169 INFO LearnReadOrientationModel - Requester pays: disabled 09:45:05.169 INFO LearnReadOrientationModel - Initializing engine 09:45:05.169 INFO LearnReadOrientationModel - Done initializing engine 09:45:05.179 INFO IOUtils - Extracting data from archive: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.f1r2.tar.gz 09:45:05.179 INFO LearnReadOrientationModel - Shutting down engine [May 5, 2023 9:45:05 AM UTC] org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2184708096 *********************************************************************** A USER ERROR has occurred: Could not extract data from: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.f1r2.tar.gz *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 09:45:07.149 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:07 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:07.326 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:07.326 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:07.327 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:07.327 INFO FilterMutectCalls - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:07.327 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:07.327 INFO FilterMutectCalls - Start Date/Time: May 5, 2023 9:45:07 AM UTC 09:45:07.327 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:07.327 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:07.327 INFO FilterMutectCalls - HTSJDK Version: 2.21.2 09:45:07.327 INFO FilterMutectCalls - Picard Version: 2.21.9 09:45:07.327 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:07.327 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:07.328 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:07.328 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:07.328 INFO FilterMutectCalls - Deflater: IntelDeflater 09:45:07.328 INFO FilterMutectCalls - Inflater: IntelInflater 09:45:07.328 INFO FilterMutectCalls - GCS max retries/reopens: 20 09:45:07.328 INFO FilterMutectCalls - Requester pays: disabled 09:45:07.328 INFO FilterMutectCalls - Initializing engine 09:45:07.601 INFO FilterMutectCalls - Shutting down engine [May 5, 2023 9:45:07 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2188902400 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 09:45:09.575 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:09 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:09.750 INFO SelectVariants - ------------------------------------------------------------ 09:45:09.750 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:09.750 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:09.750 INFO SelectVariants - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:09.750 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:09.750 INFO SelectVariants - Start Date/Time: May 5, 2023 9:45:09 AM UTC 09:45:09.751 INFO SelectVariants - ------------------------------------------------------------ 09:45:09.751 INFO SelectVariants - ------------------------------------------------------------ 09:45:09.751 INFO SelectVariants - HTSJDK Version: 2.21.2 09:45:09.751 INFO SelectVariants - Picard Version: 2.21.9 09:45:09.751 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:09.751 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:09.751 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:09.751 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:09.751 INFO SelectVariants - Deflater: IntelDeflater 09:45:09.751 INFO SelectVariants - Inflater: IntelInflater 09:45:09.751 INFO SelectVariants - GCS max retries/reopens: 20 09:45:09.751 INFO SelectVariants - Requester pays: disabled 09:45:09.751 INFO SelectVariants - Initializing engine 09:45:09.981 INFO SelectVariants - Shutting down engine [May 5, 2023 9:45:09 AM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2176843776 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. cat: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.selected.vcf: No such file or directory ---- Mutect2 Postprocessing II (Filtering out known SNV/Indel using dbSNP or the Sanger Mouse database) ---- Fri May 5 05:45:10 EDT 2023 timestamp: 1683279910 Failed to open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.postprocessed.vcf.gz: unknown file type [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.postprocessed.snp_removed.vcf.gz" : No such file or directory Failed to read from MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.postprocessed.snp_removed.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf.gz: No such file or directory ---- Mutect2 Postprocessing III (Annotate calls) ---- Fri May 5 05:45:10 EDT 2023 timestamp: 1683279910 Error : Cannot read input file 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf' Command line : SnpEff GRCm38.86 -csvStats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.annotated.vcf.stats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf snpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: snpEff [eff] [options] genome_version [input_file] variants_file : Default is STDIN Options: -chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. -classic : Use old style annotations instead of Sequence Ontology and Hgvs. -csvStats : Create CSV summary file. -download : Download reference genome if not available. Default: true -i : Input format [ vcf, bed ]. Default: VCF. -fileList : Input actually contains a list of files to process. -o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF. -s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html' -noStats : Do not create stats (summary) file Results filter options: -fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) -no-downstream : Do not show DOWNSTREAM changes -no-intergenic : Do not show INTERGENIC changes -no-intron : Do not show INTRON changes -no-upstream : Do not show UPSTREAM changes -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes -no : Do not show 'EffectType'. This option can be used several times. Annotations options: -cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false -cancerSamples : Two column TXT file defining 'oringinal \t derived' samples. -formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN'). -geneId : Use gene ID instead of gene name (VCF output). Default: false -hgvs : Use HGVS annotations for amino acid sub-field. Default: true -hgvsOld : Use old HGVS notation. Default: false -hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false -hgvsTrId : Use transcript ID in HGVS notation. Default: false -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. -noHgvs : Do not add HGVS annotations. -noLof : Do not add LOF and NMD annotations. -noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end). -oicr : Add OICR tag in VCF file. Default: false -sequenceOntology : Use Sequence Ontology terms. Default: true Generic options: -c , -config : Specify config file -configOption name=value : Override a config file option -d , -debug : Debug mode (very verbose). -dataDir : Override data_dir parameter from config file. -download : Download a SnpEff database, if not available locally. Default: true -nodownload : Do not download a SnpEff database, if not available locally. -h , -help : Show this help and exit -noLog : Do not report usage statistics to server -t : Use multiple threads (implies '-noStats'). Default 'off' -q , -quiet : Quiet mode (do not show any messages or errors) -v , -verbose : Verbose mode -version : Show version number and exit Database options: -canon : Only use canonical transcripts. -canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in . -interaction : Annotate using inteactions (requires interaciton database). Default: true -interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times) -maxTSL : Only use transcripts having Transcript Support Level lower than . -motif : Annotate using motifs (requires Motif database). Default: true -nextProt : Annotate using NextProt (requires NextProt database). -noGenome : Do not load any genomic database (e.g. annotate using custom files). -noExpandIUB : Disable IUB code expansion in input variants -noInteraction : Disable inteaction annotations -noMotif : Disable motif annotations. -noNextProt : Disable NextProt annotations. -onlyReg : Only use regulation tracks. -onlyProtein : Only use protein coding transcripts. Default: false -onlyTr : Only use the transcripts in this file. Format: One transcript ID per line. -reg : Regulation track to use (this option can be used add several times). -ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2 -spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases -spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases -spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases -strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false -ud , -upDownStreamLen : Set upstream downstream interval length (in bases) USAGE: IndexFeatureFile [arguments] Creates an index for a feature file, e.g. VCF or BED file. Version:4.1.7.0 Required Arguments: --input,-I:GATKPathSpecifier Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format Required. Optional Arguments: --arguments_file:File read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null. --gatk-config-file:String A configuration file to use with the GATK. Default value: null. --gcs-max-retries,-gcs-retries:Integer If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20. --gcs-project-for-requester-pays:String Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. Default value: . --help,-h:Boolean display the help message Default value: false. Possible values: {true, false} --output,-O:GATKPathSpecifier The output index file. If missing, the tool will create an index file in the same directory as the input file. Default value: null. --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false} --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null. --use-jdk-deflater,-jdk-deflater:Boolean Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false} --use-jdk-inflater,-jdk-inflater:Boolean Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false} --verbosity,-verbosity:LogLevel Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG} --version:Boolean display the version number for this tool Default value: false. Possible values: {true, false} Advanced Arguments: --showHidden,-showHidden:Boolean display hidden arguments Default value: false. Possible values: {true, false} *********************************************************************** A USER ERROR has occurred: V is not a recognized option *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. USAGE: IndexFeatureFile [arguments] Creates an index for a feature file, e.g. VCF or BED file. Version:4.1.7.0 Required Arguments: --input,-I:GATKPathSpecifier Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format Required. Optional Arguments: --arguments_file:File read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null. --gatk-config-file:String A configuration file to use with the GATK. Default value: null. --gcs-max-retries,-gcs-retries:Integer If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20. --gcs-project-for-requester-pays:String Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. Default value: . --help,-h:Boolean display the help message Default value: false. Possible values: {true, false} --output,-O:GATKPathSpecifier The output index file. If missing, the tool will create an index file in the same directory as the input file. Default value: null. --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false} --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null. --use-jdk-deflater,-jdk-deflater:Boolean Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false} --use-jdk-inflater,-jdk-inflater:Boolean Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false} --verbosity,-verbosity:LogLevel Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG} --version:Boolean display the version number for this tool Default value: false. Possible values: {true, false} Advanced Arguments: --showHidden,-showHidden:Boolean display hidden arguments Default value: false. Possible values: {true, false} *********************************************************************** A USER ERROR has occurred: V is not a recognized option *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. 09:45:17.263 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/DISCVRSeq-1.07/DISCVRSeq-1.07.jar!/com/intel/gkl/native/libgkl_compression.so 09:45:19.132 INFO VariantQC - ------------------------------------------------------------ 09:45:19.133 INFO VariantQC - DISCVR-seq Toolkit v1.07 09:45:19.133 INFO VariantQC - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:19.134 INFO VariantQC - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:19.134 INFO VariantQC - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:19.134 INFO VariantQC - Start Date/Time: May 5, 2023 9:45:17 AM UTC 09:45:19.134 INFO VariantQC - ------------------------------------------------------------ 09:45:19.134 INFO VariantQC - ------------------------------------------------------------ 09:45:19.134 INFO VariantQC - HTSJDK Version: 2.18.0 09:45:19.134 INFO VariantQC - Picard Version: unknown 09:45:19.134 INFO VariantQC - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:19.134 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:19.134 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:19.134 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:19.134 INFO VariantQC - Deflater: IntelDeflater 09:45:19.135 INFO VariantQC - Inflater: IntelInflater 09:45:19.135 INFO VariantQC - GCS max retries/reopens: 20 09:45:19.135 INFO VariantQC - Requester pays: disabled 09:45:19.135 INFO VariantQC - Initializing engine 09:45:19.526 INFO VariantQC - Shutting down engine [May 5, 2023 9:45:19 AM UTC] com.github.discvrseq.walkers.variantqc.VariantQC done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=2058354688 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.vcf. Error was: It doesn't exist. *********************************************************************** org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.vcf. Error was: It doesn't exist. at org.broadinstitute.hellbender.utils.io.IOUtils.assertFileIsReadable(IOUtils.java:854) at org.broadinstitute.hellbender.engine.FeatureDataSource.getCodecForFeatureInput(FeatureDataSource.java:323) at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:304) at org.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:256) at org.broadinstitute.hellbender.engine.VariantWalker.initializeDrivingVariants(VariantWalker.java:58) at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:55) at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:697) at org.broadinstitute.hellbender.engine.VariantWalker.onStartup(VariantWalker.java:45) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205) at com.github.discvrseq.Main.main(Main.java:50) 09:45:20.470 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/DISCVRSeq-1.07/DISCVRSeq-1.07.jar!/com/intel/gkl/native/libgkl_compression.so 09:45:22.076 INFO VariantQC - ------------------------------------------------------------ 09:45:22.077 INFO VariantQC - DISCVR-seq Toolkit v1.07 09:45:22.077 INFO VariantQC - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:22.077 INFO VariantQC - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:22.077 INFO VariantQC - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:22.078 INFO VariantQC - Start Date/Time: May 5, 2023 9:45:20 AM UTC 09:45:22.078 INFO VariantQC - ------------------------------------------------------------ 09:45:22.078 INFO VariantQC - ------------------------------------------------------------ 09:45:22.078 INFO VariantQC - HTSJDK Version: 2.18.0 09:45:22.078 INFO VariantQC - Picard Version: unknown 09:45:22.078 INFO VariantQC - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:22.078 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:22.078 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:22.078 INFO VariantQC - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:22.078 INFO VariantQC - Deflater: IntelDeflater 09:45:22.078 INFO VariantQC - Inflater: IntelInflater 09:45:22.078 INFO VariantQC - GCS max retries/reopens: 20 09:45:22.078 INFO VariantQC - Requester pays: disabled 09:45:22.079 INFO VariantQC - Initializing engine 09:45:22.410 INFO VariantQC - Shutting down engine [May 5, 2023 9:45:22 AM UTC] com.github.discvrseq.walkers.variantqc.VariantQC done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2058354688 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf. Error was: It doesn't exist. *********************************************************************** org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf. Error was: It doesn't exist. at org.broadinstitute.hellbender.utils.io.IOUtils.assertFileIsReadable(IOUtils.java:854) at org.broadinstitute.hellbender.engine.FeatureDataSource.getCodecForFeatureInput(FeatureDataSource.java:323) at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:304) at org.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:256) at org.broadinstitute.hellbender.engine.VariantWalker.initializeDrivingVariants(VariantWalker.java:58) at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:55) at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:697) at org.broadinstitute.hellbender.engine.VariantWalker.onStartup(VariantWalker.java:45) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205) at com.github.discvrseq.Main.main(Main.java:50) rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.read-orientation-model.tar.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.postprocessed.snp_removed.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.filtered.selected.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.filtered.selected.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.filt.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.m2.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann1.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann2.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann3.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann4.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann5.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann6.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.ann7.vcf': No such file or directory rm: cannot remove 'snpEff_summary.html': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory Error in library(SomaticSignatures) : there is no package called ‘SomaticSignatures’ Execution halted ---- Running Mutect2 (single-sample) ---- Fri May 5 05:45:23 EDT 2023 timestamp: 1683279923 09:45:25.175 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:25 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:25.351 INFO Mutect2 - ------------------------------------------------------------ 09:45:25.352 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:25.352 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:25.352 INFO Mutect2 - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:25.352 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:25.352 INFO Mutect2 - Start Date/Time: May 5, 2023 9:45:25 AM UTC 09:45:25.352 INFO Mutect2 - ------------------------------------------------------------ 09:45:25.352 INFO Mutect2 - ------------------------------------------------------------ 09:45:25.353 INFO Mutect2 - HTSJDK Version: 2.21.2 09:45:25.353 INFO Mutect2 - Picard Version: 2.21.9 09:45:25.353 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:25.353 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:25.353 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:25.353 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:25.353 INFO Mutect2 - Deflater: IntelDeflater 09:45:25.353 INFO Mutect2 - Inflater: IntelInflater 09:45:25.353 INFO Mutect2 - GCS max retries/reopens: 20 09:45:25.353 INFO Mutect2 - Requester pays: disabled 09:45:25.353 INFO Mutect2 - Initializing engine 09:45:25.410 INFO Mutect2 - Shutting down engine [May 5, 2023 9:45:25 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2193620992 *********************************************************************** A USER ERROR has occurred: Couldn't read file. Error was: MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam with exception: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Mutect2 SS Postprocessing I (OrientationFilter, Indel size selection, filtering) ---- Fri May 5 05:45:25 EDT 2023 timestamp: 1683279925 09:45:27.381 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:27 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:27.555 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:27.555 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:27.555 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:27.555 INFO FilterMutectCalls - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:27.555 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:27.555 INFO FilterMutectCalls - Start Date/Time: May 5, 2023 9:45:27 AM UTC 09:45:27.555 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:27.555 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:27.556 INFO FilterMutectCalls - HTSJDK Version: 2.21.2 09:45:27.556 INFO FilterMutectCalls - Picard Version: 2.21.9 09:45:27.556 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:27.556 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:27.556 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:27.556 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:27.556 INFO FilterMutectCalls - Deflater: IntelDeflater 09:45:27.556 INFO FilterMutectCalls - Inflater: IntelInflater 09:45:27.556 INFO FilterMutectCalls - GCS max retries/reopens: 20 09:45:27.556 INFO FilterMutectCalls - Requester pays: disabled 09:45:27.556 INFO FilterMutectCalls - Initializing engine 09:45:27.829 INFO FilterMutectCalls - Shutting down engine [May 5, 2023 9:45:27 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2161639424 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Exception in thread "main" java.lang.RuntimeException: File not found 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.vcf' at org.snpeff.util.Gpr.reader(Gpr.java:536) at org.snpeff.util.Gpr.reader(Gpr.java:507) at org.snpeff.fileIterator.MarkerFileIterator.init(MarkerFileIterator.java:63) at org.snpeff.fileIterator.FileIterator.(FileIterator.java:39) at org.snpeff.fileIterator.MarkerFileIterator.(MarkerFileIterator.java:36) at org.snpeff.fileIterator.VcfFileIterator.(VcfFileIterator.java:81) at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:145) at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:122) at org.snpsift.SnpSift.run(SnpSift.java:588) at org.snpsift.SnpSift.main(SnpSift.java:76) cp: cannot stat 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.vcf': No such file or directory cp: cannot stat 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.vcf': No such file or directory 09:45:30.008 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:30 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:30.186 INFO SelectVariants - ------------------------------------------------------------ 09:45:30.186 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:30.186 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:30.186 INFO SelectVariants - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:30.186 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:30.187 INFO SelectVariants - Start Date/Time: May 5, 2023 9:45:29 AM UTC 09:45:30.187 INFO SelectVariants - ------------------------------------------------------------ 09:45:30.187 INFO SelectVariants - ------------------------------------------------------------ 09:45:30.187 INFO SelectVariants - HTSJDK Version: 2.21.2 09:45:30.187 INFO SelectVariants - Picard Version: 2.21.9 09:45:30.187 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:30.187 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:30.187 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:30.187 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:30.187 INFO SelectVariants - Deflater: IntelDeflater 09:45:30.187 INFO SelectVariants - Inflater: IntelInflater 09:45:30.187 INFO SelectVariants - GCS max retries/reopens: 20 09:45:30.187 INFO SelectVariants - Requester pays: disabled 09:45:30.187 INFO SelectVariants - Initializing engine 09:45:30.415 INFO SelectVariants - Shutting down engine [May 5, 2023 9:45:30 AM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2181562368 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.filtered.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. cat: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.filtered.selected.vcf: No such file or directory ---- Mutect2 SS Postprocessing II (Filtering out known SNV/Indel using dbSNP or the Sanger Mouse database) ---- Fri May 5 05:45:30 EDT 2023 timestamp: 1683279930 Failed to open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.postprocessed.vcf.gz: unknown file type [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.postprocessed.snp_removed.vcf.gz" : No such file or directory Failed to read from MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.postprocessed.snp_removed.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vcf.gz: No such file or directory ---- Mutect2 SS Postprocessing III (Annotate calls) ---- Fri May 5 05:45:30 EDT 2023 timestamp: 1683279930 Error : Cannot read input file 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vcf' Command line : SnpEff GRCm38.86 -csvStats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.annotated.vcf.stats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vcf snpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: snpEff [eff] [options] genome_version [input_file] variants_file : Default is STDIN Options: -chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. -classic : Use old style annotations instead of Sequence Ontology and Hgvs. -csvStats : Create CSV summary file. -download : Download reference genome if not available. Default: true -i : Input format [ vcf, bed ]. Default: VCF. -fileList : Input actually contains a list of files to process. -o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF. -s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html' -noStats : Do not create stats (summary) file Results filter options: -fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) -no-downstream : Do not show DOWNSTREAM changes -no-intergenic : Do not show INTERGENIC changes -no-intron : Do not show INTRON changes -no-upstream : Do not show UPSTREAM changes -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes -no : Do not show 'EffectType'. This option can be used several times. Annotations options: -cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false -cancerSamples : Two column TXT file defining 'oringinal \t derived' samples. -formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN'). -geneId : Use gene ID instead of gene name (VCF output). Default: false -hgvs : Use HGVS annotations for amino acid sub-field. Default: true -hgvsOld : Use old HGVS notation. Default: false -hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false -hgvsTrId : Use transcript ID in HGVS notation. Default: false -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. -noHgvs : Do not add HGVS annotations. -noLof : Do not add LOF and NMD annotations. -noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end). -oicr : Add OICR tag in VCF file. Default: false -sequenceOntology : Use Sequence Ontology terms. Default: true Generic options: -c , -config : Specify config file -configOption name=value : Override a config file option -d , -debug : Debug mode (very verbose). -dataDir : Override data_dir parameter from config file. -download : Download a SnpEff database, if not available locally. Default: true -nodownload : Do not download a SnpEff database, if not available locally. -h , -help : Show this help and exit -noLog : Do not report usage statistics to server -t : Use multiple threads (implies '-noStats'). Default 'off' -q , -quiet : Quiet mode (do not show any messages or errors) -v , -verbose : Verbose mode -version : Show version number and exit Database options: -canon : Only use canonical transcripts. -canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in . -interaction : Annotate using inteactions (requires interaciton database). Default: true -interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times) -maxTSL : Only use transcripts having Transcript Support Level lower than . -motif : Annotate using motifs (requires Motif database). Default: true -nextProt : Annotate using NextProt (requires NextProt database). -noGenome : Do not load any genomic database (e.g. annotate using custom files). -noExpandIUB : Disable IUB code expansion in input variants -noInteraction : Disable inteaction annotations -noMotif : Disable motif annotations. -noNextProt : Disable NextProt annotations. -onlyReg : Only use regulation tracks. -onlyProtein : Only use protein coding transcripts. Default: false -onlyTr : Only use the transcripts in this file. Format: One transcript ID per line. -reg : Regulation track to use (this option can be used add several times). -ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2 -spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases -spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases -spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases -strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false -ud , -upDownStreamLen : Set upstream downstream interval length (in bases) rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.postprocessed.snp_removed.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.filtered.selected.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.filtered.selected.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.vcf.summary': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.AM.filtered.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.filt.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.m2.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann1.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann2.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann3.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann4.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann5.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann6.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.ann7.vcf': No such file or directory rm: cannot remove 'snpEff_summary.html': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory 09:45:33.678 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:33 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:33.863 INFO Mutect2 - ------------------------------------------------------------ 09:45:33.863 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:33.863 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:33.864 INFO Mutect2 - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:33.864 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:33.864 INFO Mutect2 - Start Date/Time: May 5, 2023 9:45:33 AM UTC 09:45:33.864 INFO Mutect2 - ------------------------------------------------------------ 09:45:33.864 INFO Mutect2 - ------------------------------------------------------------ 09:45:33.864 INFO Mutect2 - HTSJDK Version: 2.21.2 09:45:33.864 INFO Mutect2 - Picard Version: 2.21.9 09:45:33.864 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:33.864 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:33.864 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:33.864 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:33.864 INFO Mutect2 - Deflater: IntelDeflater 09:45:33.865 INFO Mutect2 - Inflater: IntelInflater 09:45:33.865 INFO Mutect2 - GCS max retries/reopens: 20 09:45:33.865 INFO Mutect2 - Requester pays: disabled 09:45:33.865 INFO Mutect2 - Initializing engine 09:45:33.930 INFO Mutect2 - Shutting down engine [May 5, 2023 9:45:33 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2182610944 *********************************************************************** A USER ERROR has occurred: Couldn't read file. Error was: MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam with exception: Cannot read non-existent file: file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. ---- Mutect2 SS Postprocessing I (OrientationFilter, Indel size selection, filtering) ---- Fri May 5 05:45:33 EDT 2023 timestamp: 1683279933 09:45:35.906 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:36 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:36.082 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:36.083 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:36.083 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:36.083 INFO FilterMutectCalls - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:36.083 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:36.083 INFO FilterMutectCalls - Start Date/Time: May 5, 2023 9:45:35 AM UTC 09:45:36.083 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:36.083 INFO FilterMutectCalls - ------------------------------------------------------------ 09:45:36.084 INFO FilterMutectCalls - HTSJDK Version: 2.21.2 09:45:36.084 INFO FilterMutectCalls - Picard Version: 2.21.9 09:45:36.084 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:36.084 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:36.084 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:36.084 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:36.084 INFO FilterMutectCalls - Deflater: IntelDeflater 09:45:36.084 INFO FilterMutectCalls - Inflater: IntelInflater 09:45:36.084 INFO FilterMutectCalls - GCS max retries/reopens: 20 09:45:36.084 INFO FilterMutectCalls - Requester pays: disabled 09:45:36.084 INFO FilterMutectCalls - Initializing engine 09:45:36.355 INFO FilterMutectCalls - Shutting down engine [May 5, 2023 9:45:36 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2185232384 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Exception in thread "main" java.lang.RuntimeException: File not found 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.vcf' at org.snpeff.util.Gpr.reader(Gpr.java:536) at org.snpeff.util.Gpr.reader(Gpr.java:507) at org.snpeff.fileIterator.MarkerFileIterator.init(MarkerFileIterator.java:63) at org.snpeff.fileIterator.FileIterator.(FileIterator.java:39) at org.snpeff.fileIterator.MarkerFileIterator.(MarkerFileIterator.java:36) at org.snpeff.fileIterator.VcfFileIterator.(VcfFileIterator.java:81) at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:145) at org.snpsift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:122) at org.snpsift.SnpSift.run(SnpSift.java:588) at org.snpsift.SnpSift.main(SnpSift.java:76) cp: cannot stat 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.vcf': No such file or directory cp: cannot stat 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.vcf': No such file or directory 09:45:38.554 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so May 05, 2023 9:45:38 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 09:45:38.730 INFO SelectVariants - ------------------------------------------------------------ 09:45:38.730 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.1.7.0 09:45:38.730 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:45:38.730 INFO SelectVariants - Executing as dcook@galen64 on Linux v4.18.0-348.20.1.el8_5.x86_64 amd64 09:45:38.730 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-8u265-b01-0ubuntu2~18.04-b01 09:45:38.730 INFO SelectVariants - Start Date/Time: May 5, 2023 9:45:38 AM UTC 09:45:38.730 INFO SelectVariants - ------------------------------------------------------------ 09:45:38.730 INFO SelectVariants - ------------------------------------------------------------ 09:45:38.731 INFO SelectVariants - HTSJDK Version: 2.21.2 09:45:38.731 INFO SelectVariants - Picard Version: 2.21.9 09:45:38.731 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:45:38.731 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:45:38.731 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:45:38.731 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:45:38.731 INFO SelectVariants - Deflater: IntelDeflater 09:45:38.731 INFO SelectVariants - Inflater: IntelInflater 09:45:38.731 INFO SelectVariants - GCS max retries/reopens: 20 09:45:38.731 INFO SelectVariants - Requester pays: disabled 09:45:38.731 INFO SelectVariants - Initializing engine 09:45:38.961 INFO SelectVariants - Shutting down engine [May 5, 2023 9:45:38 AM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2182610944 *********************************************************************** A USER ERROR has occurred: Couldn't read file file:///home/wranalab/dcook/projects/mouse_cna/MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.filtered.vcf. Error was: It doesn't exist. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. cat: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.filtered.selected.vcf: No such file or directory ---- Mutect2 SS Postprocessing II (Filtering out known SNV/Indel using dbSNP or the Sanger Mouse database) ---- Fri May 5 05:45:39 EDT 2023 timestamp: 1683279939 Failed to open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.postprocessed.vcf.gz: unknown file type [E::hts_open_format] Failed to open file "MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.postprocessed.snp_removed.vcf.gz" : No such file or directory Failed to read from MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.postprocessed.snp_removed.vcf.gz: No such file or directory gzip: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vcf.gz: No such file or directory ---- Mutect2 SS Postprocessing III (Annotate calls) ---- Fri May 5 05:45:39 EDT 2023 timestamp: 1683279939 Error : Cannot read input file 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vcf' Command line : SnpEff GRCm38.86 -csvStats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.annotated.vcf.stats MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vcf snpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: snpEff [eff] [options] genome_version [input_file] variants_file : Default is STDIN Options: -chr : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. -classic : Use old style annotations instead of Sequence Ontology and Hgvs. -csvStats : Create CSV summary file. -download : Download reference genome if not available. Default: true -i : Input format [ vcf, bed ]. Default: VCF. -fileList : Input actually contains a list of files to process. -o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF. -s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html' -noStats : Do not create stats (summary) file Results filter options: -fi , -filterInterval : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) -no-downstream : Do not show DOWNSTREAM changes -no-intergenic : Do not show INTERGENIC changes -no-intron : Do not show INTRON changes -no-upstream : Do not show UPSTREAM changes -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes -no : Do not show 'EffectType'. This option can be used several times. Annotations options: -cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: false -cancerSamples : Two column TXT file defining 'oringinal \t derived' samples. -formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN'). -geneId : Use gene ID instead of gene name (VCF output). Default: false -hgvs : Use HGVS annotations for amino acid sub-field. Default: true -hgvsOld : Use old HGVS notation. Default: false -hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: false -hgvsTrId : Use transcript ID in HGVS notation. Default: false -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. -noHgvs : Do not add HGVS annotations. -noLof : Do not add LOF and NMD annotations. -noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end). -oicr : Add OICR tag in VCF file. Default: false -sequenceOntology : Use Sequence Ontology terms. Default: true Generic options: -c , -config : Specify config file -configOption name=value : Override a config file option -d , -debug : Debug mode (very verbose). -dataDir : Override data_dir parameter from config file. -download : Download a SnpEff database, if not available locally. Default: true -nodownload : Do not download a SnpEff database, if not available locally. -h , -help : Show this help and exit -noLog : Do not report usage statistics to server -t : Use multiple threads (implies '-noStats'). Default 'off' -q , -quiet : Quiet mode (do not show any messages or errors) -v , -verbose : Verbose mode -version : Show version number and exit Database options: -canon : Only use canonical transcripts. -canonList : Only use canonical transcripts, replace some transcripts using the 'gene_id transcript_id' entries in . -interaction : Annotate using inteactions (requires interaciton database). Default: true -interval : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times) -maxTSL : Only use transcripts having Transcript Support Level lower than . -motif : Annotate using motifs (requires Motif database). Default: true -nextProt : Annotate using NextProt (requires NextProt database). -noGenome : Do not load any genomic database (e.g. annotate using custom files). -noExpandIUB : Disable IUB code expansion in input variants -noInteraction : Disable inteaction annotations -noMotif : Disable motif annotations. -noNextProt : Disable NextProt annotations. -onlyReg : Only use regulation tracks. -onlyProtein : Only use protein coding transcripts. Default: false -onlyTr : Only use the transcripts in this file. Format: One transcript ID per line. -reg : Regulation track to use (this option can be used add several times). -ss , -spliceSiteSize : Set size for splice sites (donor and acceptor) in bases. Default: 2 -spliceRegionExonSize : Set size for splice site region within exons. Default: 3 bases -spliceRegionIntronMin : Set minimum number of bases for splice site region within intron. Default: 3 bases -spliceRegionIntronMax : Set maximum number of bases for splice site region within intron. Default: 8 bases -strict : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false -ud , -upDownStreamLen : Set upstream downstream interval length (in bases) rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.postprocessed.snp_removed.vcf.gz': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.annotated.vcf.stats.genes.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.annotated.vcf.stats': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.filtered.selected.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.filtered.selected.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.vcf.summary': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.AM.filtered.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.filt.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.m2.vcf.idx': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann1.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann2.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann3.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann4.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann5.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann6.vcf': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.ann7.vcf': No such file or directory rm: cannot remove 'snpEff_summary.html': No such file or directory rm: cannot remove 'Mutect2FilteringStats.tsv': No such file or directory -------------------- EXCEPTION -------------------- MSG: ERROR: PolyPhen not available STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168 STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121 STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:45:40 2023 Ensembl API version = 96 --------------------------------------------------- ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vcf awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Mutect2.vep.maf (No such file or directory) -------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /home/wranalab/dcook/.vep/mus_musculus not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:45:40 2023 Ensembl API version = 96 --------------------------------------------------- -------------------- EXCEPTION -------------------- MSG: ERROR: Cache directory /home/wranalab/dcook/.vep/mus_musculus not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311 STACK Bio::EnsEMBL::VEP::CacheDir::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /opt/vep-96/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /opt/vep-96/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /opt/vep-96/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep-96/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /opt/vep-96/./vep:218 Date (localtime) = Fri May 5 05:45:41 2023 Ensembl API version = 96 --------------------------------------------------- ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vcf ERROR: Provided --input-vcf is missing or empty: MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vcf awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Normal.Mutect2.vep.maf (No such file or directory) awk: cannot open MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vep.maf (No such file or directory) mv: cannot stat 'MoCaSeq_Test/results/Mutect2/MoCaSeq_Test.Tumor.Mutect2.vep.maf.tmp': No such file or directory ---- Generate LOH data ---- Fri May 5 05:45:41 EDT 2023 timestamp: 1683279941 Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Error in `[<-.data.frame`(`*tmp*`, , "Plot_Freq", value = 0) : replacement has 1 row, data has 0 Calls: LOH_AssignStatus -> [<- -> [<-.data.frame Execution halted Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Error in file(file, "rt") : cannot open the connection Calls: ProcessCountData -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'MoCaSeq_Test.VariantsForLOH.txt': No such file or directory Execution halted ---- Generate and plot copy number data ---- Fri May 5 05:45:46 EDT 2023 timestamp: 1683279946 ---- Run CopywriteR ---- Fri May 5 05:45:46 EDT 2023 timestamp: 1683279946 Loading required package: BiocParallel Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Error in FUN(newX[, i], ...) : file 'MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam' does not exist Calls: CopywriteR -> apply -> FUN Execution halted ---- Export raw data and re-normalize using Mode ---- Fri May 5 05:45:54 EDT 2023 timestamp: 1683279954 Error in setwd(paste(path, "/", name, "/results/Copywriter/CNAprofiles/", : cannot change working directory Execution halted Traceback (most recent call last): File "/opt/MoCaSeq/repository/CNV_CopywriterGetModeCorrectionFactor.py", line 49, in CalculateMode(name) File "/opt/MoCaSeq/repository/CNV_CopywriterGetModeCorrectionFactor.py", line 40, in CalculateMode myPeak = myMode(ModeLocations) File "/opt/MoCaSeq/repository/CNV_CopywriterGetModeCorrectionFactor.py", line 18, in myMode kde = stats.gaussian_kde(sarr) File "/usr/local/lib/python2.7/dist-packages/scipy/stats/kde.py", line 195, in __init__ raise ValueError("`dataset` input should have multiple elements.") ValueError: `dataset` input should have multiple elements. Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'MoCaSeq_Test.KDEestimate.txt': No such file or directory Execution halted ---- Plot CNV-profiles ---- Fri May 5 05:45:55 EDT 2023 timestamp: 1683279955 Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Error in file(file, "rt") : cannot open the connection Calls: ProcessSegmentData -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'MoCaSeq_Test.Copywriter.segments.Mode.txt': No such file or directory Execution halted Error in file(file, "rt") : cannot open the connection Calls: read.delim -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.Copywriter.segments.Mode.txt': No such file or directory Execution halted rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome1.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome2.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome3.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome4.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome5.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome6.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome7.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome8.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome9.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome10.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome11.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome12.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome13.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome14.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome15.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome16.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome17.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome18.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome19.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome20.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome21.txt': No such file or directory rm: cannot remove 'MoCaSeq_Test/results/Copywriter/MoCaSeq_Test.SegmentsChromosome22.txt': No such file or directory ---- Run HMMCopy (bin-size 20000) ---- Fri May 5 05:46:01 EDT 2023 timestamp: 1683279961 BgzfStream ERROR: unable to open file MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam BamReader ERROR: Could not open BGZF stream for MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam Could not open input BAM files. BgzfStream ERROR: unable to open file MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam BamReader ERROR: Could not open BGZF stream for MoCaSeq_Test/results/bam/MoCaSeq_Test.Normal.bam Could not open input BAM files. ---- Plot HMMCopy ---- Fri May 5 05:46:01 EDT 2023 timestamp: 1683279961 Loading required package: data.table Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Error in (breaks[i] + 1):(breaks[i + 1] - 1) : NA/NaN argument Calls: wigsToRangedData -> wigToRangedData Execution halted Error in file(file, "rt") : cannot open the connection Calls: read.delim -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'MoCaSeq_Test/results/HMMCopy/MoCaSeq_Test.HMMCopy.20000.segments.txt': No such file or directory Execution halted ---- Run msisensor---- Fri May 5 05:46:07 EDT 2023 timestamp: 1683279967 open: No such file or directory msisensor: bamreader.cpp:181: bool ReadInBamReads(const char*, const string&, unsigned int, unsigned int, std::vector&, std::__cxx11::string): Assertion `fp' failed. /opt/MoCaSeq/MoCaSeq.sh: line 943: 675629 Aborted (core dumped) msisensor msi -n $name/results/bam/$name.Normal.bam -t $name/results/bam/$name.Tumor.bam -o $name/results/msisensor/"$name".msisensor -d $microsatellite_file -b $threads ---- Finished analysis of sample MoCaSeq_Test ---- Fri May 5 05:46:46 EDT 2023 timestamp: 1683280006