**#I am now analysing the single cell RNA seq data for the somatic mutation calling.
1. I made BAM and BAM.BAI file with minimap2 using the command below**
(minimap for fastq to SAM)
./minimap2 -a hg38.mmi xx_HL.fastq > alignment.sam
(samtools 'view' for SAM to BAM)
./samtools view -S -b ../minimap2/ESCC_align_minimap2_index_HL/20221120minimap2${file}_HL.sam> ESCC_BAM_HL/20221123BAM${file}_HL.bam
(samtools for BAM to sorted to BAI)
./samtools sort ESCC_BAM_HL/20221123BAM${file}_HL.bam -o ESCC_sorted_BAM_HL/20221201_sortedBAM${file}_HL.sorted.bam
./samtools index ESCC_sorted_BAM_HL/20221201_sortedBAM${file}_HL.sorted.bam ESCC_sorted_BAM_BAI_HL/20221201_ESCCsortedBAMBAI${file}_HL.bam.bai
#2. and used Strelka command like below (format of RESA's suggested input prerequisite for variant calling):
**#I am now analysing the single cell RNA seq data for the somatic mutation calling.
1. I made BAM and BAM.BAI file with minimap2 using the command below**
(minimap for fastq to SAM)
./minimap2 -a hg38.mmi xx_HL.fastq > alignment.sam
(samtools 'view' for SAM to BAM) ./samtools view -S -b ../minimap2/ESCC_align_minimap2_index_HL/20221120minimap2${file}_HL.sam> ESCC_BAM_HL/20221123BAM${file}_HL.bam
(samtools for BAM to sorted to BAI) ./samtools sort ESCC_BAM_HL/20221123BAM${file}_HL.bam -o ESCC_sorted_BAM_HL/20221201_sortedBAM${file}_HL.sorted.bam
./samtools index ESCC_sorted_BAM_HL/20221201_sortedBAM${file}_HL.sorted.bam ESCC_sorted_BAM_BAI_HL/20221201_ESCCsortedBAMBAI${file}_HL.bam.bai
#2. and used Strelka command like below (format of RESA's suggested input prerequisite for variant calling):
conda activate strelka; python strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py --bam 21_N4_split/AGNCGCTT.bam --referenceFasta hg38.fa --rna --runDir ./strelka_split_out/ESCC_21_N4_NUC_split_test; ./strelka_split_out/ESCC_21_N4_NUC_split_test/runWorkflow.py -m local -j 4
#Then, I got an long error like below:
[2022-12-02T04:50:53.559908Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenome Segment_chromId_000_chr1_0019' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka- 2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/ge nomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId _000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch6 0/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/j c2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4 _split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/conf ig/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:50:53.569852Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Er ror Message: [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] La st 11 stderr lines from task (of 11 total lines): [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.476438Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scrat ch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.477711Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.481713Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' whi le attempting to read BAM/CRAM file: [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.483178Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/A GNCGCTT.bam' [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.484195Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_selected_region: chr1:225245890-237101754 [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.485154Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] no bam record currently set [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.486134Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.487068Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x 86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping -quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpd ir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /g pfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.x ml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/ km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka /strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT. bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorMod el.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.488035Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] version: 2.9.10 [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.488978Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:50:53.572757Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:53.489907Z] [c23n05.ruddle.hpc.yale.i nternal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] compiler: g++-6.3.1 [2022-12-02T04:50:53.618353Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining ta sks to complete. [2022-12-02T04:50:54.358430Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenome Segment_chromId_000_chr1_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka- 2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/geno meSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing - -stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_0 00_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/ lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2 545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_s plit/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:50:54.362504Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Error Message: [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.256168Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.257477Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.266638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.267753Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.268751Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_selected_region: chr1:11854670-23710535 [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.269712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] no bam record currently set [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.270701Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.271758Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.272849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] version: 2.9.10 [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.273810Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:50:54.366525Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.274712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] compiler: g++-6.3.1 [2022-12-02T04:50:54.403870Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_001_chr10_0010' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:50:54.407493Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Error Message: [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.323526Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.327089Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.332459Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334074Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334740Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_selected_region: chr10:111497454-122648036 [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.336271Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] no bam record currently set [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.341764Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.342722Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.345071Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] version: 2.9.10 [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.346361Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:50:54.410653Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.348638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] compiler: g++-6.3.1 [2022-12-02T04:50:54.414580Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:50:54.418518Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Error Message: [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.310092Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.320856Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.326367Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.327457Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.328218Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_selected_region: chr1:35564806-47420671 [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.329242Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] no bam record currently set [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.330175Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.331350Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.332391Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] version: 2.9.10 [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.333437Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:50:54.421756Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] [2022-12-02T04:50:54.334637Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] compiler: g++-6.3.1 [2022-12-02T04:51:00.339176Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [TaskManager] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow' [2022-12-02T04:51:10.059849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors: [2022-12-02T04:51:10.063988Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGen omeSegment_chromId_000_chr1_0003' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strel ka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/g enomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasin g --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromI d_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch 60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/ jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N 4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/con fig/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:51:10.067254Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Error Message: [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.310092Z] [c23n05.ruddle.hpc.yal e.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/sc ratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.320856Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.326367Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.327457Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.328218Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] bam_stream_selected_region: chr1:35564806-47420671 [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.329242Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] no bam record currently set [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.330175Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.331350Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:35565205-47420272 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0003. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0003.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.332391Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] version: 2.9.10 [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.333437Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:51:10.070546Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334637Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0003] compiler: g++-6.3.1 [2022-12-02T04:51:10.074609Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_001_chr10_0010' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:51:10.077994Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Error Message: [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.323526Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.327089Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.332459Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334074Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.334740Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] bam_stream_selected_region: chr10:111497454-122648036 [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.336271Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] no bam record currently set [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.341764Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.342722Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr10:111497853-122647637 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_001_chr10_0010. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_001_chr10_0010.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.345071Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] version: 2.9.10 [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.346361Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:51:10.081138Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.348638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_001_chr10_0010] compiler: g++-6.3.1 [2022-12-02T04:51:10.084854Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete sub-workflow task: 'CallGenome' launched from master workflow, failed sub-workflow classname: 'CallWorkflow' [2022-12-02T04:51:10.087670Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0019' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:51:10.091207Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Error Message: [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.476438Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.477711Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.481713Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.483178Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.484195Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] bam_stream_selected_region: chr1:225245890-237101754 [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.485154Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] no bam record currently set [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.486134Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.487068Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:225246289-237101355 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0019. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0019.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.488035Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] version: 2.9.10 [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.488978Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:51:10.094060Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:53.489907Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0019] compiler: g++-6.3.1 [2022-12-02T04:51:10.097679Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0001' launched from sub-workflow 'CallGenome', error code: 1, command: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json' [2022-12-02T04:51:10.100576Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Error Message: [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] Last 11 stderr lines from task (of 11 total lines): [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.256168Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [W::hts_idx_load2] The index file is older than the data file: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam.bai [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.257477Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.266638Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file: [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.267753Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_label: '/gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam' [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.268751Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] bam_stream_selected_region: chr1:11854670-23710535 [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.269712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] no bam record currently set [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.270701Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.271758Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] cmdline: /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/libexec/starling2 --region chr1:11855069-23710136 --ref /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/hg38.fa --max-indel-size 49 --min-mapping-quality 20 --gvcf-output-prefix /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/segment.chromId_000_chr1_0001. --gvcf-min-gqx 15 --gvcf-min-homref-gqx 15 --gvcf-max-snv-strand-bias 10 --enable-read-backed-phasing --stats-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka_split_out/ESCC_21_N4_NUC_split_test/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0001.xml --het-variant-frequency-extension 0.45 --use-rna-scoring --retain-optimal-soft-clipping --snv-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNASNVScoringModels.json --indel-scoring-model-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/RNAIndelScoringModels.json --align-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/21_N4_split/AGNCGCTT.bam --gvcf-skip-header --indel-error-models-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/indelErrorModel.json --theta-file /gpfs/ycga/scratch60/lifton/jc2545/km/strelka/strelka-2.9.10.centos6_x86_64/share/config/theta.json [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.272849Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] version: 2.9.10 [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.273810Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] buildTime: 2018-11-08T00:32:40.775496Z [2022-12-02T04:51:10.103510Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [WorkflowRunner] [ERROR] [2022-12-02T04:50:54.274712Z] [c23n05.ruddle.hpc.yale.internal] [15690_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0001] compiler: g++-6.3.1
#What should I change?Thank you