[2026-06-04T19:29:04.580931Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-04T19:29:04.587528Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-04T19:29:04.587540Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-04T19:29:04.587546Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-04T19:29:04.587551Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXee4kXK'
[2026-06-04T19:29:04.587556Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-04T19:29:04.587562Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-04T19:29:04.587566Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-04T19:29:04.587569Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] memMb: 1523736
[2026-06-04T19:29:04.587573Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-04T19:29:04.587577Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-04T19:29:04.587581Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-04T19:29:04.587584Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-04T19:29:04.587588Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-04T19:29:04.588332Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-04T19:29:04.588434Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-04T19:29:04.594020Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-04T19:29:04.594744Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-04T19:29:04.594917Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-04T19:29:04.595267Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-04T19:29:04.595486Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.596404Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.596495Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.596663Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.596817Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.597046Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.597133Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.597520Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.597803Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.601153Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-04T19:29:04.610550Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.610671Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.610745Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.610831Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.610902Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.610974Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.611040Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.611118Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.611188Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:29:04.611233Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-04T19:29:04.631208Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.631468Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.631958Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.632369Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.632914Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.635145Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:29:04.637686Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:04.638722Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:29:04.639579Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:29:04.747268Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.747331Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.747580Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.747827Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.750010Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:29:04.750795Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:04.812818Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.812886Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.813140Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:29:04.815343Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:29:04.844941Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:05.910577Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:05.910917Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:29:05.913347Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:29:05.942750Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.463588Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.464150Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.466156Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:29:33.495855Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.496023Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.496148Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.496542Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.497087Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.500079Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-04T19:29:33.501384Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-04T19:29:33.502306Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-04T19:29:33.530002Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.530070Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.530098Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.530307Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.530524Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.533530Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-04T19:29:33.534218Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-04T19:29:33.562427Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.562496Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.562687Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:29:33.565051Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-04T19:29:33.594720Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:29:37.716820Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-04T19:29:52.706695Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-04T19:29:52.706695Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] 
[2026-06-04T19:29:52.706695Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-04T19:29:52.706802Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] 
[2026-06-04T19:29:52.706815Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-04T19:29:52.706824Z] [nf-d24e28e3afb000f9516150587a9c9b97-d66bc-drpjk] [682_1] [WorkflowRunner] Elapsed time for full workflow: 48 sec