File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/bf5e6cc27f3ebe986f9ba4ac74841c/.command.err
Size
16.5 KB
Attempt
[2026-06-09T03:05:50.231905Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-09T03:05:50.232994Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-09T03:05:50.233022Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-09T03:05:50.233028Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-09T03:05:50.233033Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXLmkOF0'
[2026-06-09T03:05:50.233037Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-09T03:05:50.233044Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-09T03:05:50.233048Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-09T03:05:50.233052Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-09T03:05:50.233056Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-09T03:05:50.233059Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-09T03:05:50.233063Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-09T03:05:50.233067Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-09T03:05:50.233071Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-09T03:05:50.234011Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-09T03:05:50.234069Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-09T03:05:50.239705Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-09T03:05:50.240378Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-09T03:05:50.240582Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-09T03:05:50.241052Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-09T03:05:50.241209Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.242123Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.242873Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.242987Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.243346Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.245659Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.245875Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.246187Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.246529Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.247612Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-09T03:05:50.260382Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.260540Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.260652Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.260770Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.260925Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.261125Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.261360Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.261583Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.261731Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-09T03:05:50.261935Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-09T03:05:50.277601Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.277862Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.278170Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.278570Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.279335Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.282595Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-09T03:05:50.285450Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-09T03:05:50.288773Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-09T03:05:50.289188Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-09T03:05:50.395597Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.395683Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.395988Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.396298Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.399585Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-09T03:05:50.401019Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-09T03:05:50.460772Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.460838Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.461084Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-09T03:05:50.464300Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-09T03:05:50.525699Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:51.591714Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-09T03:05:51.592070Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-09T03:05:51.594742Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-09T03:05:51.656222Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.729559Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.729972Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.732997Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-09T03:06:20.794385Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.794538Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.794654Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.795248Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.795804Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.798713Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-09T03:06:20.800181Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-09T03:06:20.801245Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-09T03:06:20.828249Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.828318Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.828340Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.828518Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.829139Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.831448Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-09T03:06:20.832426Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-09T03:06:20.862065Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.862132Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.862293Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-09T03:06:20.864796Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-09T03:06:20.894378Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-09T03:06:23.362997Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-09T03:06:38.353074Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-09T03:06:38.353074Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] 
[2026-06-09T03:06:38.353074Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-09T03:06:38.353167Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] 
[2026-06-09T03:06:38.353176Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-09T03:06:38.353183Z] [nf-83bf5e6cc27f3ebe986f9ba4ac74841c-936a1-x98bq] [658_1] [WorkflowRunner] Elapsed time for full workflow: 48 sec