.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (custom_Sig_18_tumor_normal)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/101a362418abb51764f109c578a6e0/.command.err
Size: 26.6 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (custom_Sig_18_tumor_normal)
Attempt
Content

[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXo05VBt/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.XXXXo05VBt/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.XXXXo05VBt/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.XXXXo05VBt/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.XXXXo05VBt/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[2026-06-05T15:19:02.226981Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-05T15:19:02.228406Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2026-06-05T15:19:02.228419Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-05T15:19:02.228424Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-05T15:19:02.228428Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXo05VBt'
[2026-06-05T15:19:02.228432Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/manta/runWorkflow.py -m local -j 14'
[2026-06-05T15:19:02.228437Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-05T15:19:02.228441Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] nCores: 14
[2026-06-05T15:19:02.228445Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] memMb: 3047507
[2026-06-05T15:19:02.228448Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/manta/workspace/pyflow.data
[2026-06-05T15:19:02.228452Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-05T15:19:02.228456Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-05T15:19:02.228459Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-05T15:19:02.228463Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-05T15:19:02.229386Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-05T15:19:02.229506Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2026-06-05T15:19:02.229711Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2026-06-05T15:19:02.230585Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2026-06-05T15:19:02.230803Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_001' to master workflow
[2026-06-05T15:19:02.230915Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2026-06-05T15:19:02.231186Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2026-06-05T15:19:02.231280Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2026-06-05T15:19:02.231530Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2026-06-05T15:19:02.232020Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'makeGraphTmpDir' to master workflow
[2026-06-05T15:19:02.234522Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2026-06-05T15:19:02.265838Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2026-06-05T15:19:02.266143Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2026-06-05T15:19:02.266494Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_001' from master workflow
[2026-06-05T15:19:02.269233Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2026-06-05T15:19:02.271098Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2026-06-05T15:19:02.501397Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' to master workflow
[2026-06-05T15:19:02.747663Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' to master workflow
[2026-06-05T15:19:02.747905Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding sub-workflow task 'mergeLocusGraphInputList' to master workflow
[2026-06-05T15:19:02.747994Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'mergeLocusGraph' to master workflow
[2026-06-05T15:19:02.748066Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'checkLocusGraph' to master workflow
[2026-06-05T15:19:02.748136Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'removeTmpDir' to master workflow
[2026-06-05T15:19:02.748203Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'locusGraphStats' to master workflow
[2026-06-05T15:19:02.748437Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'makeHyGenDir' to master workflow
[2026-06-05T15:19:02.748553Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'generateCandidateSV_0000' to master workflow
[2026-06-05T15:19:02.748640Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortCandidateSV' to master workflow
[2026-06-05T15:19:02.748748Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding sub-workflow task 'sortCandidateSVInputList' to master workflow
[2026-06-05T15:19:02.748816Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
[2026-06-05T15:19:02.748886Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
[2026-06-05T15:19:02.748953Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
[2026-06-05T15:19:02.749050Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
[2026-06-05T15:19:02.749122Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
[2026-06-05T15:19:02.749187Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
[2026-06-05T15:19:02.749296Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortSomaticSV' to master workflow
[2026-06-05T15:19:02.749398Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding sub-workflow task 'sortSomaticSVInputList' to master workflow
[2026-06-05T15:19:02.749465Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'sort_sortSomaticSV' to master workflow
[2026-06-05T15:19:02.749597Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'tabix_sortSomaticSV' to master workflow
[2026-06-05T15:19:02.749674Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
[2026-06-05T15:19:02.749740Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
[2026-06-05T15:19:02.749837Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
[2026-06-05T15:19:02.749907Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
[2026-06-05T15:19:02.749949Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-05T15:19:05.767225Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2026-06-05T15:19:16.433710Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_001' launched from master workflow
[2026-06-05T15:19:16.434830Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2026-06-05T15:19:16.437641Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2026-06-05T15:19:16.466769Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2026-06-05T15:19:16.467132Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2026-06-05T15:19:16.467433Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'makeGraphTmpDir' from master workflow
[2026-06-05T15:19:16.467928Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2026-06-05T15:19:16.470742Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2026-06-05T15:19:16.472768Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:summarizeStats] Task initiated on local node
[2026-06-05T15:19:16.473389Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:makeGraphTmpDir] Task initiated on local node
[2026-06-05T15:19:16.500257Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2026-06-05T15:19:16.501982Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2026-06-05T15:19:16.502014Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'makeGraphTmpDir' launched from master workflow
[2026-06-05T15:19:16.502292Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' from master workflow
[2026-06-05T15:19:16.502801Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' from master workflow
[2026-06-05T15:19:16.534579Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000] Task initiated on local node
[2026-06-05T15:19:16.535706Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000] Task initiated on local node
[2026-06-05T15:19:34.023584Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' launched from master workflow
[2026-06-05T15:19:45.241280Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' launched from master workflow
[2026-06-05T15:19:45.242144Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching sub-workflow task: 'mergeLocusGraphInputList' from master workflow
[2026-06-05T15:19:45.242570Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:mergeLocusGraphInputList] Starting task specification for sub-workflow
[2026-06-05T15:19:45.242848Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:mergeLocusGraphInputList] Finished task specification for sub-workflow
[2026-06-05T15:19:45.243854Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed sub-workflow task: 'mergeLocusGraphInputList' launched from master workflow
[2026-06-05T15:19:45.244150Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'mergeLocusGraph' from master workflow
[2026-06-05T15:19:45.247524Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:mergeLocusGraph] Task initiated on local node
[2026-06-05T15:19:45.308513Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'mergeLocusGraph' launched from master workflow
[2026-06-05T15:19:45.308893Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'checkLocusGraph' from master workflow
[2026-06-05T15:19:45.309290Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'locusGraphStats' from master workflow
[2026-06-05T15:19:45.311006Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'removeTmpDir' from master workflow
[2026-06-05T15:19:45.314095Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:checkLocusGraph] Task initiated on local node
[2026-06-05T15:19:45.314551Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:locusGraphStats] Task initiated on local node
[2026-06-05T15:19:45.344240Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:removeTmpDir] Task initiated on local node
[2026-06-05T15:19:45.344833Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'checkLocusGraph' launched from master workflow
[2026-06-05T15:19:45.344945Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'locusGraphStats' launched from master workflow
[2026-06-05T15:19:45.345429Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'makeHyGenDir' from master workflow
[2026-06-05T15:19:45.345691Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'removeTmpDir' launched from master workflow
[2026-06-05T15:19:45.347989Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:makeHyGenDir] Task initiated on local node
[2026-06-05T15:19:45.377760Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'makeHyGenDir' launched from master workflow
[2026-06-05T15:19:45.378083Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow
[2026-06-05T15:19:45.381285Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node
[2026-06-05T15:19:51.194826Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'generateCandidateSV_0000' launched from master workflow
[2026-06-05T15:19:51.195231Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching sub-workflow task: 'sortEdgeRuntimeLogsInputList' from master workflow
[2026-06-05T15:19:51.195721Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Starting task specification for sub-workflow
[2026-06-05T15:19:51.196055Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'fixVcfHeader_sortCandidateSV' from master workflow
[2026-06-05T15:19:51.196427Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Finished task specification for sub-workflow
[2026-06-05T15:19:51.196736Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'fixVcfHeader_sortDiploidSV' from master workflow
[2026-06-05T15:19:51.197355Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'fixVcfHeader_sortSomaticSV' from master workflow
[2026-06-05T15:19:51.200378Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed sub-workflow task: 'sortEdgeRuntimeLogsInputList' launched from master workflow
[2026-06-05T15:19:51.200810Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:fixVcfHeader_sortCandidateSV] Task initiated on local node
[2026-06-05T15:19:51.203619Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:fixVcfHeader_sortSomaticSV] Task initiated on local node
[2026-06-05T15:19:51.203859Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'sortEdgeRuntimeLogs' from master workflow
[2026-06-05T15:19:51.206738Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortEdgeRuntimeLogs] Task initiated on local node
[2026-06-05T15:19:51.237989Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:fixVcfHeader_sortDiploidSV] Task initiated on local node
[2026-06-05T15:19:51.268284Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'sortEdgeRuntimeLogs' launched from master workflow
[2026-06-05T15:19:51.268392Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'fixVcfHeader_sortDiploidSV' launched from master workflow
[2026-06-05T15:19:51.268433Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'fixVcfHeader_sortSomaticSV' launched from master workflow
[2026-06-05T15:19:51.268472Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'fixVcfHeader_sortCandidateSV' launched from master workflow
[2026-06-05T15:19:51.268986Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching sub-workflow task: 'sortDiploidSVInputList' from master workflow
[2026-06-05T15:19:51.269332Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortDiploidSVInputList] Starting task specification for sub-workflow
[2026-06-05T15:19:51.269595Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching sub-workflow task: 'sortCandidateSVInputList' from master workflow
[2026-06-05T15:19:51.269873Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortCandidateSVInputList] Starting task specification for sub-workflow
[2026-06-05T15:19:51.270092Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching sub-workflow task: 'sortSomaticSVInputList' from master workflow
[2026-06-05T15:19:51.270356Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortDiploidSVInputList] Finished task specification for sub-workflow
[2026-06-05T15:19:51.270683Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortSomaticSVInputList] Starting task specification for sub-workflow
[2026-06-05T15:19:51.270900Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortCandidateSVInputList] Finished task specification for sub-workflow
[2026-06-05T15:19:51.271266Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed sub-workflow task: 'sortDiploidSVInputList' launched from master workflow
[2026-06-05T15:19:51.271376Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sortSomaticSVInputList] Finished task specification for sub-workflow
[2026-06-05T15:19:51.271475Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed sub-workflow task: 'sortCandidateSVInputList' launched from master workflow
[2026-06-05T15:19:51.271547Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed sub-workflow task: 'sortSomaticSVInputList' launched from master workflow
[2026-06-05T15:19:51.271749Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'sort_sortDiploidSV' from master workflow
[2026-06-05T15:19:51.272022Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'sort_sortCandidateSV' from master workflow
[2026-06-05T15:19:51.272518Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'sort_sortSomaticSV' from master workflow
[2026-06-05T15:19:51.275379Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sort_sortDiploidSV] Task initiated on local node
[2026-06-05T15:19:51.278005Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sort_sortCandidateSV] Task initiated on local node
[2026-06-05T15:19:51.279117Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:sort_sortSomaticSV] Task initiated on local node
[2026-06-05T15:19:51.340708Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'sort_sortDiploidSV' launched from master workflow
[2026-06-05T15:19:51.340775Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'sort_sortCandidateSV' launched from master workflow
[2026-06-05T15:19:51.340798Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'sort_sortSomaticSV' launched from master workflow
[2026-06-05T15:19:51.341025Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'extractSmallIndels' from master workflow
[2026-06-05T15:19:51.341522Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'tabix_sortDiploidSV' from master workflow
[2026-06-05T15:19:51.342059Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'tabix_sortCandidateSV' from master workflow
[2026-06-05T15:19:51.342588Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'tabix_sortSomaticSV' from master workflow
[2026-06-05T15:19:51.347205Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:extractSmallIndels] Task initiated on local node
[2026-06-05T15:19:51.347654Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:tabix_sortSomaticSV] Task initiated on local node
[2026-06-05T15:19:51.348705Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:tabix_sortCandidateSV] Task initiated on local node
[2026-06-05T15:19:51.349787Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:tabix_sortDiploidSV] Task initiated on local node
[2026-06-05T15:19:51.375418Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'tabix_sortSomaticSV' launched from master workflow
[2026-06-05T15:19:51.375492Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'tabix_sortCandidateSV' launched from master workflow
[2026-06-05T15:19:51.376775Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'tabix_sortDiploidSV' launched from master workflow
[2026-06-05T15:19:51.384253Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'extractSmallIndels' launched from master workflow
[2026-06-05T15:19:51.384465Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Launching command task: 'extractSmallIndels_tabix' from master workflow
[2026-06-05T15:19:51.387047Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskRunner:extractSmallIndels_tabix] Task initiated on local node
[2026-06-05T15:19:51.416661Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [TaskManager] Completed command task: 'extractSmallIndels_tabix' launched from master workflow
[2026-06-05T15:20:05.899100Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Manta workflow successfully completed.
[2026-06-05T15:20:05.899100Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] 
[2026-06-05T15:20:05.899100Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] 	workflow version: 1.6.0
[2026-06-05T15:20:05.899269Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] 
[2026-06-05T15:20:05.899286Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-05T15:20:05.899292Z] [nf-dc101a362418abb51764f109c578a6e0-d18b6-mwqx4] [603_1] [WorkflowRunner] Elapsed time for full workflow: 63 sec