.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_34799195-34799564.bed)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/9ea004813d1722cc06ff2f22ca940e/.command.err
Size: 16.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (HCC1395_tumor_vs_HCC1395_BL;chr21_34799195-34799564.bed)
Attempt
Content

[2026-05-28T23:03:03.762535Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T23:03:03.772205Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T23:03:03.772233Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T23:03:03.772239Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T23:03:03.772245Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXnwAhFB'
[2026-05-28T23:03:03.772251Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T23:03:03.772257Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T23:03:03.772263Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T23:03:03.772267Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] memMb: 1523801
[2026-05-28T23:03:03.772274Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T23:03:03.772279Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T23:03:03.772284Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T23:03:03.772289Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T23:03:03.772294Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T23:03:03.772701Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T23:03:03.772841Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T23:03:03.780850Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T23:03:03.781750Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T23:03:03.781943Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T23:03:03.782195Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T23:03:03.782456Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.783843Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.783975Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.784141Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.784636Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.785046Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.785211Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.787352Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.787918Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T23:03:03.788064Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.804699Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805009Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805097Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805209Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805301Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805399Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805483Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805582Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805671Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:03.805731Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T23:03:03.821752Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.822107Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.822535Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.823155Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.823835Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.829083Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:03.830570Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:03.830790Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:03.831416Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:03.939691Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.939763Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.940115Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.940394Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:03.943506Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:03.944492Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:04.004264Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:04.004332Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:04.004636Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:04.007107Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:04.068390Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.433951Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.434352Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.436892Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:05.498251Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.016660Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.017344Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.019919Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:42.049088Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.049272Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.049423Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.049696Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.050028Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.053875Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T23:03:42.054347Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T23:03:42.055047Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T23:03:42.082297Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.082343Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.082377Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.082595Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.082865Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.085236Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T23:03:42.086124Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T23:03:42.114726Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.114779Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.114986Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:42.117052Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T23:03:42.146682Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:51.917419Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T23:04:06.890914Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T23:04:06.890914Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] 
[2026-05-28T23:04:06.890914Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T23:04:06.890990Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] 
[2026-05-28T23:04:06.890997Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T23:04:06.891006Z] [nf-769ea004813d1722cc06ff2f22ca940e-2b196-7n5w6] [839_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec