[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXs5VIJX/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXs5VIJX/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXs5VIJX/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXs5VIJX/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXs5VIJX/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[2026-06-08T20:42:55.981624Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-08T20:42:55.985484Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2026-06-08T20:42:55.985512Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-08T20:42:55.985519Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-08T20:42:55.985524Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXs5VIJX'
[2026-06-08T20:42:55.985529Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/manta/runWorkflow.py -m local -j 14'
[2026-06-08T20:42:55.985538Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-08T20:42:55.985543Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] nCores: 14
[2026-06-08T20:42:55.985547Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-08T20:42:55.985551Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/manta/workspace/pyflow.data
[2026-06-08T20:42:55.985555Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-08T20:42:55.985558Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-08T20:42:55.985562Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-08T20:42:55.985566Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-08T20:42:55.986155Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-08T20:42:55.986268Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2026-06-08T20:42:55.986572Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2026-06-08T20:42:55.987154Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2026-06-08T20:42:55.987427Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_001' to master workflow
[2026-06-08T20:42:55.987597Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2026-06-08T20:42:55.987818Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2026-06-08T20:42:55.988032Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2026-06-08T20:42:55.988337Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2026-06-08T20:42:55.988853Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'makeGraphTmpDir' to master workflow
[2026-06-08T20:42:55.992794Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2026-06-08T20:42:56.057504Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2026-06-08T20:42:56.058638Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_001' from master workflow
[2026-06-08T20:42:56.060029Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2026-06-08T20:42:56.064447Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2026-06-08T20:42:56.068255Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2026-06-08T20:42:56.358896Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' to master workflow
[2026-06-08T20:42:56.683311Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' to master workflow
[2026-06-08T20:42:56.683719Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding sub-workflow task 'mergeLocusGraphInputList' to master workflow
[2026-06-08T20:42:56.683829Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'mergeLocusGraph' to master workflow
[2026-06-08T20:42:56.683908Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'checkLocusGraph' to master workflow
[2026-06-08T20:42:56.683989Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'removeTmpDir' to master workflow
[2026-06-08T20:42:56.684063Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'locusGraphStats' to master workflow
[2026-06-08T20:42:56.684359Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'makeHyGenDir' to master workflow
[2026-06-08T20:42:56.684511Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'generateCandidateSV_0000' to master workflow
[2026-06-08T20:42:56.684627Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.684754Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding sub-workflow task 'sortCandidateSVInputList' to master workflow
[2026-06-08T20:42:56.684829Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.684902Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
[2026-06-08T20:42:56.684976Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.685086Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
[2026-06-08T20:42:56.685167Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.685239Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
[2026-06-08T20:42:56.685311Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.685421Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding sub-workflow task 'sortSomaticSVInputList' to master workflow
[2026-06-08T20:42:56.685487Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'sort_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.685559Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'tabix_sortSomaticSV' to master workflow
[2026-06-08T20:42:56.685637Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
[2026-06-08T20:42:56.685698Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
[2026-06-08T20:42:56.685796Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
[2026-06-08T20:42:56.685867Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
[2026-06-08T20:42:56.685912Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-08T20:42:59.271749Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2026-06-08T20:43:03.046173Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_001' launched from master workflow
[2026-06-08T20:43:03.046660Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2026-06-08T20:43:03.049699Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2026-06-08T20:43:03.111059Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2026-06-08T20:43:03.111470Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'makeGraphTmpDir' from master workflow
[2026-06-08T20:43:03.112025Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2026-06-08T20:43:03.113888Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2026-06-08T20:43:03.115507Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:summarizeStats] Task initiated on local node
[2026-06-08T20:43:03.117439Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:makeGraphTmpDir] Task initiated on local node
[2026-06-08T20:43:03.118633Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2026-06-08T20:43:03.147534Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'makeGraphTmpDir' launched from master workflow
[2026-06-08T20:43:03.147607Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2026-06-08T20:43:03.147950Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' from master workflow
[2026-06-08T20:43:03.148624Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' from master workflow
[2026-06-08T20:43:03.149925Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2026-06-08T20:43:03.165343Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000] Task initiated on local node
[2026-06-08T20:43:03.166201Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000] Task initiated on local node
[2026-06-08T20:43:13.465929Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' launched from master workflow
[2026-06-08T20:43:20.284226Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' launched from master workflow
[2026-06-08T20:43:20.285114Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching sub-workflow task: 'mergeLocusGraphInputList' from master workflow
[2026-06-08T20:43:20.285464Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:mergeLocusGraphInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:20.285747Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:mergeLocusGraphInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:20.286815Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed sub-workflow task: 'mergeLocusGraphInputList' launched from master workflow
[2026-06-08T20:43:20.287150Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'mergeLocusGraph' from master workflow
[2026-06-08T20:43:20.290463Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:mergeLocusGraph] Task initiated on local node
[2026-06-08T20:43:20.351633Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'mergeLocusGraph' launched from master workflow
[2026-06-08T20:43:20.351985Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'locusGraphStats' from master workflow
[2026-06-08T20:43:20.352545Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'checkLocusGraph' from master workflow
[2026-06-08T20:43:20.355607Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'removeTmpDir' from master workflow
[2026-06-08T20:43:20.355997Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:locusGraphStats] Task initiated on local node
[2026-06-08T20:43:20.356443Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:checkLocusGraph] Task initiated on local node
[2026-06-08T20:43:20.358845Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:removeTmpDir] Task initiated on local node
[2026-06-08T20:43:20.387846Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'locusGraphStats' launched from master workflow
[2026-06-08T20:43:20.387911Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'checkLocusGraph' launched from master workflow
[2026-06-08T20:43:20.387932Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'removeTmpDir' launched from master workflow
[2026-06-08T20:43:20.388223Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'makeHyGenDir' from master workflow
[2026-06-08T20:43:20.391370Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:makeHyGenDir] Task initiated on local node
[2026-06-08T20:43:20.420507Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'makeHyGenDir' launched from master workflow
[2026-06-08T20:43:20.420819Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow
[2026-06-08T20:43:20.423392Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node
[2026-06-08T20:43:24.595266Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'generateCandidateSV_0000' launched from master workflow
[2026-06-08T20:43:24.595650Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching sub-workflow task: 'sortEdgeRuntimeLogsInputList' from master workflow
[2026-06-08T20:43:24.595912Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:24.596269Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'fixVcfHeader_sortSomaticSV' from master workflow
[2026-06-08T20:43:24.596482Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:24.596914Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'fixVcfHeader_sortDiploidSV' from master workflow
[2026-06-08T20:43:24.597503Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'fixVcfHeader_sortCandidateSV' from master workflow
[2026-06-08T20:43:24.601006Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed sub-workflow task: 'sortEdgeRuntimeLogsInputList' launched from master workflow
[2026-06-08T20:43:24.601589Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:fixVcfHeader_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:24.601703Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'sortEdgeRuntimeLogs' from master workflow
[2026-06-08T20:43:24.602089Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:fixVcfHeader_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:24.604509Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:fixVcfHeader_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:24.605327Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortEdgeRuntimeLogs] Task initiated on local node
[2026-06-08T20:43:24.665979Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'fixVcfHeader_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:24.666036Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'fixVcfHeader_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:24.666059Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'sortEdgeRuntimeLogs' launched from master workflow
[2026-06-08T20:43:24.666079Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'fixVcfHeader_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:24.666293Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching sub-workflow task: 'sortSomaticSVInputList' from master workflow
[2026-06-08T20:43:24.666501Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortSomaticSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:24.666641Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching sub-workflow task: 'sortDiploidSVInputList' from master workflow
[2026-06-08T20:43:24.666786Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortDiploidSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:24.666934Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching sub-workflow task: 'sortCandidateSVInputList' from master workflow
[2026-06-08T20:43:24.667208Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortSomaticSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:24.667489Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortDiploidSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:24.667793Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortCandidateSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:43:24.667973Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed sub-workflow task: 'sortSomaticSVInputList' launched from master workflow
[2026-06-08T20:43:24.668001Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed sub-workflow task: 'sortDiploidSVInputList' launched from master workflow
[2026-06-08T20:43:24.668226Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'sort_sortSomaticSV' from master workflow
[2026-06-08T20:43:24.668621Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sortCandidateSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:43:24.668743Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'sort_sortDiploidSV' from master workflow
[2026-06-08T20:43:24.670670Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed sub-workflow task: 'sortCandidateSVInputList' launched from master workflow
[2026-06-08T20:43:24.672481Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sort_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:24.672907Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'sort_sortCandidateSV' from master workflow
[2026-06-08T20:43:24.673454Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sort_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:24.675557Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:sort_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:24.736879Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'sort_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:24.736947Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'sort_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:24.736969Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'sort_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:24.737178Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'tabix_sortCandidateSV' from master workflow
[2026-06-08T20:43:24.737542Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'tabix_sortDiploidSV' from master workflow
[2026-06-08T20:43:24.737912Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'tabix_sortSomaticSV' from master workflow
[2026-06-08T20:43:24.740818Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'extractSmallIndels' from master workflow
[2026-06-08T20:43:24.741140Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:tabix_sortSomaticSV] Task initiated on local node
[2026-06-08T20:43:24.742953Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:tabix_sortCandidateSV] Task initiated on local node
[2026-06-08T20:43:24.744303Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:tabix_sortDiploidSV] Task initiated on local node
[2026-06-08T20:43:24.745357Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:extractSmallIndels] Task initiated on local node
[2026-06-08T20:43:24.775285Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'tabix_sortCandidateSV' launched from master workflow
[2026-06-08T20:43:24.775359Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'tabix_sortDiploidSV' launched from master workflow
[2026-06-08T20:43:24.775386Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'tabix_sortSomaticSV' launched from master workflow
[2026-06-08T20:43:24.807178Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'extractSmallIndels' launched from master workflow
[2026-06-08T20:43:24.807451Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Launching command task: 'extractSmallIndels_tabix' from master workflow
[2026-06-08T20:43:24.809958Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskRunner:extractSmallIndels_tabix] Task initiated on local node
[2026-06-08T20:43:24.840840Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [TaskManager] Completed command task: 'extractSmallIndels_tabix' launched from master workflow
[2026-06-08T20:43:29.816593Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Manta workflow successfully completed.
[2026-06-08T20:43:29.816593Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] 
[2026-06-08T20:43:29.816593Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] 	workflow version: 1.6.0
[2026-06-08T20:43:29.816676Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] 
[2026-06-08T20:43:29.816687Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-08T20:43:29.816693Z] [nf-d3e3ed9d55ac1f3dfe6a268d860125cc-7fc2e-ttkzd] [643_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec