Entering edit mode
9 months ago
sarahgzb
▴
40
Hi guys, I'm trying to run strelka2 somatic workflow on my matched normal-tumor samples, but I keep running into the following error:
[TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_002_chr3_0015' from sub-workflow 'CallGenome'
[TaskRunner:CallGenome+callGenomeSegment_chromId_002_chr3_0015] Task initiated on local node
[TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_002_chr3_0015' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/sgheze/scratch/strelka/strelka/libexec/strelka2 --region chr3:174966672-186631115 --ref /lustre04/scratch/sgheze/strelka/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa --max-indel-size 49 --call-regions-bed /lustre04/scratch/sgheze/strelka/remapped_S07604624_Padded_primaryOnly.bed --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/sgheze/scratch/strelka/strelka/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/sgheze/scratch/strelka/strelka/share/config/somaticIndelScoringModels.json --normal-align-file /home/sgheze/scratch/strelka/B_Analysis_ready_BAM/NB007-N1_exome_ready.bam --tumor-align-file /home/sgheze/scratch/strelka/B_Analysis_ready_BAM/NB007-T1_exome_ready.bam --somatic-snv-file /lustre04/scratch/sgheze/strelka/Strelka_runs/NB007/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_002_chr3_0015.vcf --somatic-indel-file /lustre04/scratch/sgheze/strelka/Strelka_runs/NB007/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_002_chr3_0015.vcf --stats-file /lustre04/scratch/sgheze/strelka/Strelka_runs/NB007/workspace/genomeSegment.tmpdir/runStats.chromId_002_chr3_0015.xml --strelka-skip-header'
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] Error Message:
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] Anomalous task wrapper stderr output. Wrapper signal file: '/lustre04/scratch/sgheze/strelka/Strelka_runs/NB007/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/117/pyflowTaskWrapper.signal.txt'
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] Logging 6 line(s) of task wrapper log output below:
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] [2023-07-12T19:23:18.264110Z] [bc11319.int.ets1.calculquebec.ca] [43278_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_002_chr3_0015] [wrapperSignal] wrapperStart
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] [2023-07-12T19:23:27.022613Z] [bc11319.int.ets1.calculquebec.ca] [43278_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_002_chr3_0015] [wrapperSignal] taskStart
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] [2023-07-12T19:23:36.021555Z] [bc11319.int.ets1.calculquebec.ca] [43278_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_002_chr3_0015] [wrapperSignal] taskExitCode -11
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] [2023-07-12T19:23:41.327964Z] [bc11319.int.ets1.calculquebec.ca] [43278_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_002_chr3_0015] [wrapperSignal] taskStderrTail 2
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] Last 1 stderr lines from task (of 1 total lines)
[TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] [taskWrapper-stderr] [2023-07-12T19:23:33.905528Z] [bc11319.int.ets1.calculquebec.ca] [43278_1] [CallGenome+callGenomeSegment_chromId_002_chr3_0015] WARNING: theta parameter file was not given. Using internal theta values
[TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
long story short, the specific error in question is taskExitCode -11, something to do with a theta parameter file, but looking through the strelka docs I can't seem to find anything related to that. Has anyone come across this error and/or have any suggestions on how to proceed? Any help would be very much appreciated :)
