[2026-06-04T19:29:52.524492Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-04T19:29:52.525896Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-04T19:29:52.525920Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-04T19:29:52.525927Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-04T19:29:52.525933Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXTfYLZc'
[2026-06-04T19:29:52.525939Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-04T19:29:52.525946Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-04T19:29:52.525952Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-04T19:29:52.525957Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] memMb: 1015785
[2026-06-04T19:29:52.525963Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-04T19:29:52.525969Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-04T19:29:52.525974Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-04T19:29:52.525979Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-04T19:29:52.525985Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-04T19:29:52.526540Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-04T19:29:52.526600Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-04T19:29:52.534495Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-04T19:29:52.535371Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-04T19:29:52.535505Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-04T19:29:52.535659Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-04T19:29:52.535856Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.537397Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.539684Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.540248Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.540513Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-04T19:29:52.540646Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.540909Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.541015Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.541187Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.541280Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561160Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561334Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561437Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561562Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561667Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561765Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561857Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.561962Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.562059Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:29:52.562124Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-04T19:29:52.572745Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.573145Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.573818Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.574257Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.574897Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.579947Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:29:52.580760Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:29:52.583285Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:52.584345Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:29:52.690580Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.690666Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.690695Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.691096Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.691390Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.691722Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.695163Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:52.696821Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:29:52.697174Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:29:52.757586Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.757699Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.761273Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.761738Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:52.765078Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:52.875882Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.551790Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.552526Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.555014Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:30:26.616552Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.616774Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.616953Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.617292Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.617815Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.620698Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-04T19:30:26.621709Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-04T19:30:26.622557Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-04T19:30:26.650277Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.650474Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.650890Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.651130Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.651545Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.654104Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-04T19:30:26.654440Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-04T19:30:26.684408Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.684491Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.684767Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:30:26.687337Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-04T19:30:26.716985Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:30:40.692765Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-04T19:30:55.645117Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-04T19:30:55.645117Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] 
[2026-06-04T19:30:55.645117Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-04T19:30:55.645193Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] 
[2026-06-04T19:30:55.645202Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-04T19:30:55.645214Z] [nf-967890ca97e0052d384c9cacbc127640-fd160-c6c78] [696_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec