[2026-06-04T19:33:25.633176Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-04T19:33:25.633820Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-04T19:33:25.633834Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-04T19:33:25.633841Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-04T19:33:25.633847Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXEKPUwW'
[2026-06-04T19:33:25.633852Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-04T19:33:25.633859Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-04T19:33:25.633864Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-04T19:33:25.633869Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] memMb: 1523736
[2026-06-04T19:33:25.633874Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-04T19:33:25.633885Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-04T19:33:25.633890Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-04T19:33:25.633896Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-04T19:33:25.633902Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-04T19:33:25.634306Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-04T19:33:25.634411Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-04T19:33:25.640550Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-04T19:33:25.641326Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-04T19:33:25.641594Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-04T19:33:25.641854Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-04T19:33:25.642147Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.643135Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.643238Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.643572Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.643935Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.645832Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.647343Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.647690Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-04T19:33:25.648190Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.648467Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.668810Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669026Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669149Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669284Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669473Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669676Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.669889Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.670340Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.670886Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:33:25.671013Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-04T19:33:25.687651Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.688121Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.688496Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.688967Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.689917Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.694288Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:33:25.697108Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:33:25.698531Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:33:25.699516Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:25.805070Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.805574Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:33:25.808407Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:33:25.869794Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.687644Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.688153Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.690805Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:27.752140Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.752575Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.755105Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:27.816573Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.980707Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.981149Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:33:27.984172Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:33:28.013181Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.480985Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.481791Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.484185Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:33:39.545899Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.546124Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.546306Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.546633Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.547055Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.550984Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-04T19:33:39.552149Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-04T19:33:39.553057Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-04T19:33:39.612928Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.613027Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.613058Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.613333Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.613648Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.616532Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-04T19:33:39.617358Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-04T19:33:39.677825Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.677918Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.678189Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:33:39.680361Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-04T19:33:39.710179Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:44.583477Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-04T19:33:58.720517Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-04T19:33:58.720517Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] 
[2026-06-04T19:33:58.720517Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-04T19:33:58.720636Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] 
[2026-06-04T19:33:58.720646Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-04T19:33:58.720656Z] [nf-da7a2a31e7b556ab26f2e7aa14723768-66d72-69ldt] [793_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec