File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/fa2e99154c2f36bd982effc8ef5d66/.command.err
Size
16.5 KB
Attempt
[2026-05-28T23:03:02.706948Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Initiating pyFlow run
[2026-05-28T23:03:02.707974Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-05-28T23:03:02.708001Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-05-28T23:03:02.708006Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-05-28T23:03:02.708010Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXNEletO'
[2026-05-28T23:03:02.708014Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-05-28T23:03:02.708019Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] mode: local
[2026-05-28T23:03:02.708023Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-05-28T23:03:02.708026Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] memMb: 386708
[2026-05-28T23:03:02.708029Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-05-28T23:03:02.708033Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-05-28T23:03:02.708036Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-05-28T23:03:02.708040Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-05-28T23:03:02.708043Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-05-28T23:03:02.708938Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-05-28T23:03:02.708998Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-05-28T23:03:02.714770Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-05-28T23:03:02.715499Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-05-28T23:03:02.715715Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-05-28T23:03:02.715945Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-05-28T23:03:02.716174Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.717107Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.717210Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.717459Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.717764Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.717875Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.718023Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.718146Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.718222Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.732239Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.732355Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.732467Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.732584Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.733177Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.733804Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.734049Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.734313Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-05-28T23:03:02.734621Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.734722Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-05-28T23:03:02.734778Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-05-28T23:03:02.767263Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.767540Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.768238Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.768895Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.769710Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.772040Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:02.772879Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:03:02.775284Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:02.775673Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:02.887218Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.887285Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.887539Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.888185Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.890543Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:02.891561Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-05-28T23:03:02.922471Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.938112Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.938365Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-05-28T23:03:02.940541Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-05-28T23:03:03.003133Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.822838Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.823167Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-05-28T23:03:05.825500Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-05-28T23:03:05.855232Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.132873Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.133332Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.135980Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-05-28T23:05:20.197183Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.197361Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.197498Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.197906Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.198321Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.201232Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-05-28T23:05:20.202516Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-05-28T23:05:20.203405Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-05-28T23:05:20.231751Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.231814Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.231840Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.232053Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.232457Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.234865Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-05-28T23:05:20.235726Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-05-28T23:05:20.264233Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.265470Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.265638Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.268057Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-05-28T23:05:20.297359Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-05-28T23:05:20.961689Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-05-28T23:05:35.928504Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-05-28T23:05:35.928504Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] 
[2026-05-28T23:05:35.928504Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-05-28T23:05:35.928594Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] 
[2026-05-28T23:05:35.928603Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-05-28T23:05:35.928609Z] [nf-1efa2e99154c2f36bd982effc8ef5d66-156f5-nfjx4] [683_1] [WorkflowRunner] Elapsed time for full workflow: 153 sec