.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (custom_Sig_18_tumor_normal;chr21_5117003-5117331.bed)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/a9a0b9e56164ff220f02be82ff1843/.command.err
Size: 16.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (custom_Sig_18_tumor_normal;chr21_5117003-5117331.bed)
Attempt
Content

[2026-05-28T23:03:03.015294Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T23:03:03.015951Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T23:03:03.015964Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T23:03:03.015968Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T23:03:03.015972Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXt4eOrE'
[2026-05-28T23:03:03.015976Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T23:03:03.015980Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T23:03:03.015984Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T23:03:03.015988Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] memMb: 386708
[2026-05-28T23:03:03.015991Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T23:03:03.015995Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T23:03:03.015998Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T23:03:03.016002Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T23:03:03.016006Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T23:03:03.016855Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T23:03:03.016955Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T23:03:03.022425Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T23:03:03.023130Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T23:03:03.023933Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T23:03:03.024167Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T23:03:03.024345Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.024917Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.027180Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T23:03:03.027492Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.027670Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.027751Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.027897Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.027979Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.028098Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.028167Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041245Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041342Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041411Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041493Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041564Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041632Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041697Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041773Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041842Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.041887Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T23:03:03.057768Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.058027Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.058547Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.059067Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.060364Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.060945Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:03.063623Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:03.065281Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:03.066006Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:03.176189Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.176574Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.179400Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:03.240893Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:06.661656Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:06.662017Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:06.664668Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:06.726337Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:06.726669Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:06.729303Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:06.790928Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:08.809250Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:08.809606Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:08.812150Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:08.841664Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.614142Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.614903Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.617110Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:37.646890Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.647030Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.647136Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.647574Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.647901Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.651322Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T23:03:37.651671Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T23:03:37.653771Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T23:03:37.681491Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.681562Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.681584Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.681756Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.682243Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.685022Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T23:03:37.685890Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T23:03:37.715161Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.715232Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.715400Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:37.717516Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T23:03:37.747986Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:51.168787Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T23:04:06.135345Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T23:04:06.135345Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] 
[2026-05-28T23:04:06.135345Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T23:04:06.135427Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] 
[2026-05-28T23:04:06.135437Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T23:04:06.135443Z] [nf-26a9a0b9e56164ff220f02be82ff1843-e1fe1-htl27] [655_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec