.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/2d/429c9f391322f1bd28932cff45866d/.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

[2026-06-05T02:47:00.936981Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-05T02:47:00.944214Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-05T02:47:00.944246Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-05T02:47:00.944252Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-05T02:47:00.944256Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXFsjbFi'
[2026-06-05T02:47:00.944260Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-05T02:47:00.944265Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-05T02:47:00.944269Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-05T02:47:00.944272Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] memMb: 761785
[2026-06-05T02:47:00.944276Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-05T02:47:00.944279Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-05T02:47:00.944283Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-05T02:47:00.944287Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-05T02:47:00.944290Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-05T02:47:00.945135Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-05T02:47:00.945211Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-05T02:47:00.951205Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-05T02:47:00.951951Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-05T02:47:00.952143Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-05T02:47:00.952368Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-05T02:47:00.952609Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.953566Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.953661Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.953884Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.954161Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.954248Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.954407Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.954530Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.954606Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.957574Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-05T02:47:00.968266Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968418Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968495Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968595Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968669Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968742Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968810Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968886Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.968957Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-05T02:47:00.969004Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-05T02:47:00.980754Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.981006Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.981655Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.983301Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.983612Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T02:47:00.984134Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T02:47:00.986969Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T02:47:00.988243Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T02:47:00.988993Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T02:47:01.049434Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:01.049716Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-05T02:47:01.052278Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-05T02:47:01.113609Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:04.534925Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:04.535271Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T02:47:04.537750Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T02:47:04.599206Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:04.599464Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-05T02:47:04.601740Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-05T02:47:04.663552Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:06.631504Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:06.631781Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-05T02:47:06.633958Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-05T02:47:06.663603Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.537930Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.538965Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.541190Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-05T02:47:35.570862Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.571010Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.571117Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.571716Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.572977Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.573551Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-05T02:47:35.575469Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-05T02:47:35.576289Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-05T02:47:35.605312Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.605372Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.605393Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.605560Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.606031Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.608114Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-05T02:47:35.608967Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-05T02:47:35.638735Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.638794Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.638953Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-05T02:47:35.640881Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-05T02:47:35.670710Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-05T02:47:49.091416Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-05T02:48:04.063787Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-05T02:48:04.063787Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] 
[2026-06-05T02:48:04.063787Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-05T02:48:04.063865Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] 
[2026-06-05T02:48:04.063873Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-05T02:48:04.063879Z] [nf-2d429c9f391322f1bd28932cff45866d-74bd7-xn2zg] [678_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec