.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:STRELKA_SOMATIC (custom_Sig_18_tumor_normal;chr21_44102678-44103072.bed)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/7570e06e229b65f51c745c34997088/.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_44102678-44103072.bed)
Attempt
Content

[2026-06-08T20:44:42.901212Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-08T20:44:42.902513Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-08T20:44:42.902544Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-08T20:44:42.902551Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-08T20:44:42.902556Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXLcIfJe'
[2026-06-08T20:44:42.902560Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-08T20:44:42.902567Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-08T20:44:42.902571Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-08T20:44:42.902575Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-08T20:44:42.902579Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-08T20:44:42.902582Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-08T20:44:42.902586Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-08T20:44:42.902590Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-08T20:44:42.902594Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-08T20:44:42.903054Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-08T20:44:42.903115Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-08T20:44:42.908967Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-08T20:44:42.909718Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-08T20:44:42.910016Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-08T20:44:42.910300Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.910672Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-08T20:44:42.911524Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.913868Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914039Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914123Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914351Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-08T20:44:42.914531Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914613Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914726Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.914792Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.925709Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.925803Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.925871Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.925952Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926022Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926091Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926155Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926228Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926297Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-08T20:44:42.926340Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-08T20:44:42.938502Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.938795Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.939612Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.941233Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.941810Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-08T20:44:42.943839Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-08T20:44:42.944874Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:42.948167Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-08T20:44:42.949336Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-08T20:44:43.009189Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.009513Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.011809Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-08T20:44:43.025239Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.025316Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.025580Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.026819Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.028816Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-08T20:44:43.029718Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:43.042936Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.058625Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.074218Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.074488Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:43.076893Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:43.138659Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.304609Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.305316Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.308332Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-08T20:45:08.369900Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.370059Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.370185Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.370772Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.371519Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.374269Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-08T20:45:08.375011Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-08T20:45:08.376972Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-08T20:45:08.406560Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.406635Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.406658Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.406843Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.407437Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.410087Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-08T20:45:08.411033Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-08T20:45:08.440673Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.440741Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.440918Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-08T20:45:08.443213Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-08T20:45:08.473755Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:16.043062Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-08T20:45:31.022033Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-08T20:45:31.022033Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] 
[2026-06-08T20:45:31.022033Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-08T20:45:31.022146Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] 
[2026-06-08T20:45:31.022154Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-08T20:45:31.022163Z] [nf-dc7570e06e229b65f51c745c34997088-6bab7-n6zf4] [706_1] [WorkflowRunner] Elapsed time for full workflow: 48 sec