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Test strelka #33

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mvdbeek opened this issue Mar 21, 2022 · 9 comments
Closed

Test strelka #33

mvdbeek opened this issue Mar 21, 2022 · 9 comments

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@mvdbeek
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mvdbeek commented Mar 21, 2022

No description provided.

@mvdbeek
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mvdbeek commented Mar 21, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_germline/strelka_germline/2.9.10+galaxy0

@mvdbeek
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mvdbeek commented Mar 21, 2022

/run_tool_test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0

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mvdbeek commented Mar 21, 2022

waiting for cvmfs ...

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mvdbeek commented Mar 26, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_germline/strelka_germline/2.9.10+galaxy0

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mvdbeek commented Mar 26, 2022

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 3
Error 0
Failure 0
Skipped 0
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/strelka_germline/strelka_germline (Test tool test #1)

    Command Line:

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    Exit Code:
    

      

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      0
      

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    Standard Error:
    

      

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      [2022-03-26T18:00:43.994552Z] [roundup62] [7610_1] [WorkflowRunner] Initiating pyFlow run
[2022-03-26T18:00:43.995228Z] [roundup62] [7610_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaGermlineWorkflow
[2022-03-26T18:00:43.995593Z] [roundup62] [7610_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2022-03-26T18:00:43.995912Z] [roundup62] [7610_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2022-03-26T18:00:43.996224Z] [roundup62] [7610_1] [WorkflowRunner] WorkingDir: '/corral4/main/jobs/041/590/41590460/working'
[2022-03-26T18:00:43.996637Z] [roundup62] [7610_1] [WorkflowRunner] ProcessCmdLine: 'results/runWorkflow.py -m local -j 1 -g 7680'
[2022-03-26T18:00:43.996958Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] mode: local
[2022-03-26T18:00:43.997268Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] nCores: 1
[2022-03-26T18:00:43.997609Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] memMb: 7864320
[2022-03-26T18:00:43.998045Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] dataDir: /corral4/main/jobs/041/590/41590460/working/results/workspace/pyflow.data
[2022-03-26T18:00:43.998359Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2022-03-26T18:00:43.998670Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] isContinue: False
[2022-03-26T18:00:43.998989Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2022-03-26T18:00:43.999488Z] [roundup62] [7610_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2022-03-26T18:00:44.000408Z] [roundup62] [7610_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2022-03-26T18:00:44.000835Z] [roundup62] [7610_1] [StrelkaGermlineWorkflow] Initiating Strelka germline workflow version: 2.9.10
[2022-03-26T18:00:44.001808Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_makeTmpDir' to master workflow
[2022-03-26T18:00:44.002536Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_makeTmpDir' to master workflow
[2022-03-26T18:00:44.003426Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_estimateChromDepth_000_demo20' to master workflow
[2022-03-26T18:00:44.004288Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_catChromDepth' to master workflow
[2022-03-26T18:00:44.005850Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_makeTmpDir' to master workflow
[2022-03-26T18:00:44.006626Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_estimateChromDepth_000_demo20' to master workflow
[2022-03-26T18:00:44.007659Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_catChromDepth' to master workflow
[2022-03-26T18:00:44.008223Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample002_makeTmpDir' to master workflow
[2022-03-26T18:00:44.008921Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample002_estimateChromDepth_000_demo20' to master workflow
[2022-03-26T18:00:44.009644Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_sample002_catChromDepth' to master workflow
[2022-03-26T18:00:44.010376Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_mergeChromDepth' to master workflow
[2022-03-26T18:00:44.011193Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'getChromDepth_removeTmpDir' to master workflow
[2022-03-26T18:00:44.012375Z] [roundup62] [7610_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2022-03-26T18:00:44.012994Z] [roundup62] [7610_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2022-03-26T18:00:44.014832Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_makeTmpDir' from master workflow
[2022-03-26T18:00:44.027185Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:44.429783Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
[2022-03-26T18:00:44.434223Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample002_makeTmpDir' from master workflow
[2022-03-26T18:00:44.444326Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample002_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:44.799865Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample002_makeTmpDir' launched from master workflow
[2022-03-26T18:00:44.801113Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample002_estimateChromDepth_000_demo20' from master workflow
[2022-03-26T18:00:44.839593Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample002_estimateChromDepth_000_demo20] Task initiated on local node
[2022-03-26T18:00:45.316349Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample002_estimateChromDepth_000_demo20' launched from master workflow
[2022-03-26T18:00:45.325636Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
[2022-03-26T18:00:45.346261Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:45.746239Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2022-03-26T18:00:45.747310Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_demo20' from master workflow
[2022-03-26T18:00:45.761237Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_demo20] Task initiated on local node
[2022-03-26T18:00:46.214084Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample000_estimateChromDepth_000_demo20' launched from master workflow
[2022-03-26T18:00:46.215071Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2022-03-26T18:00:46.225539Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2022-03-26T18:00:46.630414Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2022-03-26T18:00:46.631388Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample001_makeTmpDir' from master workflow
[2022-03-26T18:00:46.639747Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample001_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:46.996141Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample001_makeTmpDir' launched from master workflow
[2022-03-26T18:00:46.998101Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample001_estimateChromDepth_000_demo20' from master workflow
[2022-03-26T18:00:47.014358Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample001_estimateChromDepth_000_demo20] Task initiated on local node
[2022-03-26T18:00:47.465644Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample001_estimateChromDepth_000_demo20' launched from master workflow
[2022-03-26T18:00:47.466555Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample001_catChromDepth' from master workflow
[2022-03-26T18:00:47.497277Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample001_catChromDepth] Task initiated on local node
[2022-03-26T18:00:48.040979Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample001_catChromDepth' launched from master workflow
[2022-03-26T18:00:48.088757Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_sample002_catChromDepth' from master workflow
[2022-03-26T18:00:48.116965Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_sample002_catChromDepth] Task initiated on local node
[2022-03-26T18:00:48.661852Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_sample002_catChromDepth' launched from master workflow
[2022-03-26T18:00:48.681446Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2022-03-26T18:00:48.700888Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2022-03-26T18:00:49.260014Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2022-03-26T18:00:49.263430Z] [roundup62] [7610_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2022-03-26T18:00:49.284055Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2022-03-26T18:00:49.286924Z] [roundup62] [7610_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2022-03-26T18:00:49.295645Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.314627Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.315753Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.321710Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.330265Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.336068Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S3' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.343882Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.354923Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+variants_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.359432Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+variants_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.369865Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.377305Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.378019Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+addLegacyOutputLink' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.378739Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.380297Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.380910Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S3_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.381575Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S3_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.382195Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.382798Z] [roundup62] [7610_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:49.383300Z] [roundup62] [7610_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2022-03-26T18:00:49.388828Z] [roundup62] [7610_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2022-03-26T18:00:49.702935Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2022-03-26T18:00:49.703995Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:49.712128Z] [roundup62] [7610_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2022-03-26T18:00:50.018649Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.019852Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.029834Z] [roundup62] [7610_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_demo20_0000] Task initiated on local node
[2022-03-26T18:00:51.700259Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.721775Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.739885Z] [roundup62] [7610_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2] Task initiated on local node
[2022-03-26T18:00:52.243271Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.246964Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.258631Z] [roundup62] [7610_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants] Task initiated on local node
[2022-03-26T18:00:52.714690Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.716308Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.723511Z] [roundup62] [7610_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1] Task initiated on local node
[2022-03-26T18:00:53.181481Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.185647Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S3' from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.201348Z] [roundup62] [7610_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S3] Task initiated on local node
[2022-03-26T18:00:53.702666Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S3' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.703493Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.704179Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.717716Z] [roundup62] [7610_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2022-03-26T18:00:54.169543Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.171523Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.181712Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S2_concat_vcf] Task initiated on local node
[2022-03-26T18:00:54.538269Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.539249Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.550929Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S2_index_vcf] Task initiated on local node
[2022-03-26T18:00:54.954881Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.956936Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+variants_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.972578Z] [roundup62] [7610_1] [TaskRunner:CallGenome+variants_concat_vcf] Task initiated on local node
[2022-03-26T18:00:55.322003Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+variants_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:55.324646Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+variants_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:55.353652Z] [roundup62] [7610_1] [TaskRunner:CallGenome+variants_index_vcf] Task initiated on local node
[2022-03-26T18:00:55.747912Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+variants_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:55.748824Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:55.755102Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S1_concat_vcf] Task initiated on local node
[2022-03-26T18:00:56.063570Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:56.064492Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:56.072476Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S1_index_vcf] Task initiated on local node
[2022-03-26T18:00:56.429288Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:56.431066Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+addLegacyOutputLink' from sub-workflow 'CallGenome'
[2022-03-26T18:00:56.439651Z] [roundup62] [7610_1] [TaskRunner:CallGenome+addLegacyOutputLink] Task initiated on local node
[2022-03-26T18:00:57.046235Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+addLegacyOutputLink' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:57.059010Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S3_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:57.252465Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S3_concat_vcf] Task initiated on local node
[2022-03-26T18:00:57.954239Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S3_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:57.976023Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S3_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:58.000589Z] [roundup62] [7610_1] [TaskRunner:CallGenome+gVCF_S3_index_vcf] Task initiated on local node
[2022-03-26T18:00:58.867260Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S3_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:58.906837Z] [roundup62] [7610_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:58.932290Z] [roundup62] [7610_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2022-03-26T18:00:59.531097Z] [roundup62] [7610_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:59.955075Z] [roundup62] [7610_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2022-03-26T18:01:02.953336Z] [roundup62] [7610_1] [WorkflowRunner] Strelka germline workflow successfully completed.
[2022-03-26T18:01:02.953336Z] [roundup62] [7610_1] [WorkflowRunner] 
[2022-03-26T18:01:02.953336Z] [roundup62] [7610_1] [WorkflowRunner] 	workflow version: 2.9.10
[2022-03-26T18:01:02.956238Z] [roundup62] [7610_1] [WorkflowRunner] 
[2022-03-26T18:01:02.956783Z] [roundup62] [7610_1] [WorkflowRunner] Workflow successfully completed all tasks
[2022-03-26T18:01:02.957810Z] [roundup62] [7610_1] [WorkflowRunner] Elapsed time for full workflow: 19 sec

      

      • 

    

    Standard Output:
    

      

    • 

      Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/corral4/main/jobs/041/590/41590460/working/results/runWorkflow.py

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
ref_cond
{"__current_case__": 1, "ref": {"values": [{"id": 94817815, "src": "hda"}]}, "ref_sel": "history"}

      

      
optimization
""

      

      
expert_settings
{"evs": {"__current_case__": 1, "indelScoringModelFile": null, "reportEVSFeatures": "false", "selector": "enableEVS", "snvScoringModelFile": null}, "s_e_e": "--disableSequenceErrorEstimation"}

      

      
regions
{"__current_case__": 0, "restrict_to_region": "genome"}

      

      
forced_regions
[]

      

      
pl
{"callContinuousVf": "", "ploidy": null}

      

      
oo
{"gvcf": {"__current_case__": 1, "emit_gvcfs": "yes", "noCompress": null}, "vcf_type": "false"}

      

      
strelka
{"maxIndelSize": "49", "minMapq": "20"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/strelka_germline/strelka_germline (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      [2022-03-26T18:00:31.372401Z] [roundup64] [19169_1] [WorkflowRunner] Initiating pyFlow run
[2022-03-26T18:00:31.372904Z] [roundup64] [19169_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaGermlineWorkflow
[2022-03-26T18:00:31.373277Z] [roundup64] [19169_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2022-03-26T18:00:31.373654Z] [roundup64] [19169_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2022-03-26T18:00:31.374023Z] [roundup64] [19169_1] [WorkflowRunner] WorkingDir: '/corral4/main/jobs/041/590/41590459/working'
[2022-03-26T18:00:31.374389Z] [roundup64] [19169_1] [WorkflowRunner] ProcessCmdLine: 'results/runWorkflow.py -m local -j 1 -g 7680'
[2022-03-26T18:00:31.374760Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] mode: local
[2022-03-26T18:00:31.375144Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] nCores: 1
[2022-03-26T18:00:31.375505Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] memMb: 7864320
[2022-03-26T18:00:31.375865Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] dataDir: /corral4/main/jobs/041/590/41590459/working/results/workspace/pyflow.data
[2022-03-26T18:00:31.376218Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2022-03-26T18:00:31.376619Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] isContinue: False
[2022-03-26T18:00:31.376985Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2022-03-26T18:00:31.377552Z] [roundup64] [19169_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2022-03-26T18:00:31.378481Z] [roundup64] [19169_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2022-03-26T18:00:31.379075Z] [roundup64] [19169_1] [StrelkaGermlineWorkflow] Initiating Strelka germline workflow version: 2.9.10
[2022-03-26T18:00:31.379983Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_makeTmpDir' to master workflow
[2022-03-26T18:00:31.380938Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_makeTmpDir' to master workflow
[2022-03-26T18:00:31.381875Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_estimateChromDepth_000_demo20' to master workflow
[2022-03-26T18:00:31.382634Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_catChromDepth' to master workflow
[2022-03-26T18:00:31.383428Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_makeTmpDir' to master workflow
[2022-03-26T18:00:31.384195Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_estimateChromDepth_000_demo20' to master workflow
[2022-03-26T18:00:31.385139Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_sample001_catChromDepth' to master workflow
[2022-03-26T18:00:31.385997Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_mergeChromDepth' to master workflow
[2022-03-26T18:00:31.386870Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'getChromDepth_removeTmpDir' to master workflow
[2022-03-26T18:00:31.388004Z] [roundup64] [19169_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2022-03-26T18:00:31.388740Z] [roundup64] [19169_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2022-03-26T18:00:31.389993Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_makeTmpDir' from master workflow
[2022-03-26T18:00:31.397524Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:31.554413Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
[2022-03-26T18:00:31.555617Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
[2022-03-26T18:00:31.562464Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:31.720176Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2022-03-26T18:00:31.721300Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample000_estimateChromDepth_000_demo20' from master workflow
[2022-03-26T18:00:31.728537Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample000_estimateChromDepth_000_demo20] Task initiated on local node
[2022-03-26T18:00:31.885680Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample000_estimateChromDepth_000_demo20' launched from master workflow
[2022-03-26T18:00:31.886552Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample000_catChromDepth' from master workflow
[2022-03-26T18:00:31.895189Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample000_catChromDepth] Task initiated on local node
[2022-03-26T18:00:32.651844Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample000_catChromDepth' launched from master workflow
[2022-03-26T18:00:32.652975Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample001_makeTmpDir' from master workflow
[2022-03-26T18:00:32.659386Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample001_makeTmpDir] Task initiated on local node
[2022-03-26T18:00:32.817529Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample001_makeTmpDir' launched from master workflow
[2022-03-26T18:00:32.818562Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample001_estimateChromDepth_000_demo20' from master workflow
[2022-03-26T18:00:32.825901Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample001_estimateChromDepth_000_demo20] Task initiated on local node
[2022-03-26T18:00:32.983168Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample001_estimateChromDepth_000_demo20' launched from master workflow
[2022-03-26T18:00:32.984231Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_sample001_catChromDepth' from master workflow
[2022-03-26T18:00:32.990808Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_sample001_catChromDepth] Task initiated on local node
[2022-03-26T18:00:33.248879Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_sample001_catChromDepth' launched from master workflow
[2022-03-26T18:00:33.250134Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_mergeChromDepth' from master workflow
[2022-03-26T18:00:33.259236Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_mergeChromDepth] Task initiated on local node
[2022-03-26T18:00:33.515183Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_mergeChromDepth' launched from master workflow
[2022-03-26T18:00:33.516074Z] [roundup64] [19169_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2022-03-26T18:00:33.516840Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'getChromDepth_removeTmpDir' from master workflow
[2022-03-26T18:00:33.517409Z] [roundup64] [19169_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2022-03-26T18:00:33.518143Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.518986Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.519635Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.520328Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.521351Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.522048Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.523155Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+variants_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.525624Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+variants_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.526374Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.526958Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.527672Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+addLegacyOutputLink' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.528528Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.529369Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.530080Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.530830Z] [roundup64] [19169_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:33.531463Z] [roundup64] [19169_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2022-03-26T18:00:33.533141Z] [roundup64] [19169_1] [TaskRunner:getChromDepth_removeTmpDir] Task initiated on local node
[2022-03-26T18:00:33.696937Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'getChromDepth_removeTmpDir' launched from master workflow
[2022-03-26T18:00:33.699276Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:33.706016Z] [roundup64] [19169_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2022-03-26T18:00:33.863956Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:33.865334Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' from sub-workflow 'CallGenome'
[2022-03-26T18:00:33.874236Z] [roundup64] [19169_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_demo20_0000] Task initiated on local node
[2022-03-26T18:00:35.582947Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:35.584323Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' from sub-workflow 'CallGenome'
[2022-03-26T18:00:35.591625Z] [roundup64] [19169_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1] Task initiated on local node
[2022-03-26T18:00:35.850468Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:35.852342Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' from sub-workflow 'CallGenome'
[2022-03-26T18:00:35.860883Z] [roundup64] [19169_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2] Task initiated on local node
[2022-03-26T18:00:36.068334Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.102516Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.135205Z] [roundup64] [19169_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants] Task initiated on local node
[2022-03-26T18:00:36.325527Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.326353Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.327076Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+variants_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.333541Z] [roundup64] [19169_1] [TaskRunner:CallGenome+variants_concat_vcf] Task initiated on local node
[2022-03-26T18:00:36.491523Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+variants_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.492663Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+variants_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.500066Z] [roundup64] [19169_1] [TaskRunner:CallGenome+variants_index_vcf] Task initiated on local node
[2022-03-26T18:00:36.657277Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+variants_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.658483Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.665440Z] [roundup64] [19169_1] [TaskRunner:CallGenome+gVCF_S2_concat_vcf] Task initiated on local node
[2022-03-26T18:00:36.823096Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.824446Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.831913Z] [roundup64] [19169_1] [TaskRunner:CallGenome+gVCF_S1_concat_vcf] Task initiated on local node
[2022-03-26T18:00:36.989223Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:36.990386Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.114981Z] [roundup64] [19169_1] [TaskRunner:CallGenome+gVCF_S1_index_vcf] Task initiated on local node
[2022-03-26T18:00:37.309138Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.312740Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+addLegacyOutputLink' from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.319835Z] [roundup64] [19169_1] [TaskRunner:CallGenome+addLegacyOutputLink] Task initiated on local node
[2022-03-26T18:00:37.477464Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+addLegacyOutputLink' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.478598Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.485260Z] [roundup64] [19169_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2022-03-26T18:00:37.643195Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.644270Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.651327Z] [roundup64] [19169_1] [TaskRunner:CallGenome+gVCF_S2_index_vcf] Task initiated on local node
[2022-03-26T18:00:37.808891Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.809933Z] [roundup64] [19169_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:37.816884Z] [roundup64] [19169_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2022-03-26T18:00:37.974621Z] [roundup64] [19169_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:39.140897Z] [roundup64] [19169_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2022-03-26T18:00:41.913736Z] [roundup64] [19169_1] [WorkflowRunner] Strelka germline workflow successfully completed.
[2022-03-26T18:00:41.913736Z] [roundup64] [19169_1] [WorkflowRunner] 
[2022-03-26T18:00:41.913736Z] [roundup64] [19169_1] [WorkflowRunner] 	workflow version: 2.9.10
[2022-03-26T18:00:41.914261Z] [roundup64] [19169_1] [WorkflowRunner] 
[2022-03-26T18:00:41.914643Z] [roundup64] [19169_1] [WorkflowRunner] Workflow successfully completed all tasks
[2022-03-26T18:00:41.915026Z] [roundup64] [19169_1] [WorkflowRunner] Elapsed time for full workflow: 10 sec

      

      • 

    

    Standard Output:
    

      

    • 

      Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/corral4/main/jobs/041/590/41590459/working/results/runWorkflow.py

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
ref_cond
{"__current_case__": 1, "ref": {"values": [{"id": 94817815, "src": "hda"}]}, "ref_sel": "history"}

      

      
optimization
""

      

      
expert_settings
{"evs": {"__current_case__": 1, "indelScoringModelFile": null, "reportEVSFeatures": "false", "selector": "enableEVS", "snvScoringModelFile": null}, "s_e_e": "--disableSequenceErrorEstimation"}

      

      
regions
{"__current_case__": 0, "restrict_to_region": "genome"}

      

      
forced_regions
[]

      

      
pl
{"callContinuousVf": "", "ploidy": null}

      

      
oo
{"gvcf": {"__current_case__": 0, "emit_gvcfs": "no"}, "vcf_type": "true"}

      

      
strelka
{"maxIndelSize": "49", "minMapq": "20"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"cram"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/strelka_germline/strelka_germline (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      WARNING: Cannot estimate sequence errors from data due to small or overly fragmented reference sequence. Sequence error estimation disabled.
[2022-03-26T18:00:44.040886Z] [roundup62] [7614_1] [WorkflowRunner] Initiating pyFlow run
[2022-03-26T18:00:44.045026Z] [roundup62] [7614_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaGermlineWorkflow
[2022-03-26T18:00:44.045492Z] [roundup62] [7614_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2022-03-26T18:00:44.045854Z] [roundup62] [7614_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2022-03-26T18:00:44.046210Z] [roundup62] [7614_1] [WorkflowRunner] WorkingDir: '/corral4/main/jobs/041/590/41590461/working'
[2022-03-26T18:00:44.046715Z] [roundup62] [7614_1] [WorkflowRunner] ProcessCmdLine: 'results/runWorkflow.py -m local -j 1 -g 7680'
[2022-03-26T18:00:44.047070Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] mode: local
[2022-03-26T18:00:44.047423Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] nCores: 1
[2022-03-26T18:00:44.047794Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] memMb: 7864320
[2022-03-26T18:00:44.048152Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] dataDir: /corral4/main/jobs/041/590/41590461/working/results/workspace/pyflow.data
[2022-03-26T18:00:44.048534Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2022-03-26T18:00:44.048984Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] isContinue: False
[2022-03-26T18:00:44.049342Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2022-03-26T18:00:44.049734Z] [roundup62] [7614_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2022-03-26T18:00:44.054211Z] [roundup62] [7614_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2022-03-26T18:00:44.058978Z] [roundup62] [7614_1] [StrelkaGermlineWorkflow] Initiating Strelka germline workflow version: 2.9.10
[2022-03-26T18:00:44.063423Z] [roundup62] [7614_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2022-03-26T18:00:44.064854Z] [roundup62] [7614_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2022-03-26T18:00:44.065780Z] [roundup62] [7614_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2022-03-26T18:00:44.066489Z] [roundup62] [7614_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2022-03-26T18:00:44.067274Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.068988Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.070503Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:44.071075Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.072195Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.073423Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.074303Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.075588Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+variants_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.076944Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+variants_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.078360Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.079803Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S1_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.081345Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+addLegacyOutputLink' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.082858Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_concat_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.090586Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+gVCF_S2_index_vcf' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.091748Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.092659Z] [roundup62] [7614_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2022-03-26T18:00:44.093417Z] [roundup62] [7614_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2022-03-26T18:00:44.101411Z] [roundup62] [7614_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2022-03-26T18:00:44.671630Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:44.674464Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' from sub-workflow 'CallGenome'
[2022-03-26T18:00:44.689743Z] [roundup62] [7614_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_demo20_0000] Task initiated on local node
[2022-03-26T18:00:47.300667Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_000_demo20_0000' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:47.308687Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' from sub-workflow 'CallGenome'
[2022-03-26T18:00:47.318603Z] [roundup62] [7614_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants] Task initiated on local node
[2022-03-26T18:00:48.075283Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_variants' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:48.082520Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' from sub-workflow 'CallGenome'
[2022-03-26T18:00:48.119149Z] [roundup62] [7614_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1] Task initiated on local node
[2022-03-26T18:00:48.860701Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S1' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:48.862220Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' from sub-workflow 'CallGenome'
[2022-03-26T18:00:48.881604Z] [roundup62] [7614_1] [TaskRunner:CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2] Task initiated on local node
[2022-03-26T18:00:49.832107Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+compressGenomeSegment_chromId_000_demo20_0000_gVCF_S2' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:49.849693Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:49.851858Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+variants_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:49.872546Z] [roundup62] [7614_1] [TaskRunner:CallGenome+variants_concat_vcf] Task initiated on local node
[2022-03-26T18:00:50.326449Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+variants_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.332934Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+variants_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.348615Z] [roundup62] [7614_1] [TaskRunner:CallGenome+variants_index_vcf] Task initiated on local node
[2022-03-26T18:00:50.848293Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+variants_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.860113Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:50.877929Z] [roundup62] [7614_1] [TaskRunner:CallGenome+gVCF_S2_concat_vcf] Task initiated on local node
[2022-03-26T18:00:51.336117Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.337420Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S2_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.348406Z] [roundup62] [7614_1] [TaskRunner:CallGenome+gVCF_S2_index_vcf] Task initiated on local node
[2022-03-26T18:00:51.903094Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S2_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.905203Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_concat_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:51.929287Z] [roundup62] [7614_1] [TaskRunner:CallGenome+gVCF_S1_concat_vcf] Task initiated on local node
[2022-03-26T18:00:52.526961Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_concat_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.537058Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+gVCF_S1_index_vcf' from sub-workflow 'CallGenome'
[2022-03-26T18:00:52.548178Z] [roundup62] [7614_1] [TaskRunner:CallGenome+gVCF_S1_index_vcf] Task initiated on local node
[2022-03-26T18:00:53.102620Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+gVCF_S1_index_vcf' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.108477Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.145830Z] [roundup62] [7614_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2022-03-26T18:00:53.739335Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.740502Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2022-03-26T18:00:53.751443Z] [roundup62] [7614_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2022-03-26T18:00:54.306004Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.307073Z] [roundup62] [7614_1] [TaskManager] Launching command task: 'CallGenome+addLegacyOutputLink' from sub-workflow 'CallGenome'
[2022-03-26T18:00:54.317500Z] [roundup62] [7614_1] [TaskRunner:CallGenome+addLegacyOutputLink] Task initiated on local node
[2022-03-26T18:00:54.973893Z] [roundup62] [7614_1] [TaskManager] Completed command task: 'CallGenome+addLegacyOutputLink' launched from sub-workflow 'CallGenome'
[2022-03-26T18:01:02.985008Z] [roundup62] [7614_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2022-03-26T18:01:17.202263Z] [roundup62] [7614_1] [WorkflowRunner] Strelka germline workflow successfully completed.
[2022-03-26T18:01:17.202263Z] [roundup62] [7614_1] [WorkflowRunner] 
[2022-03-26T18:01:17.202263Z] [roundup62] [7614_1] [WorkflowRunner] 	workflow version: 2.9.10
[2022-03-26T18:01:17.220693Z] [roundup62] [7614_1] [WorkflowRunner] 
[2022-03-26T18:01:17.221594Z] [roundup62] [7614_1] [WorkflowRunner] Workflow successfully completed all tasks
[2022-03-26T18:01:17.246525Z] [roundup62] [7614_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec

      

      • 

    

    Standard Output:
    

      

    • 

      Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/corral4/main/jobs/041/590/41590461/working/results/runWorkflow.py

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
ref_cond
{"__current_case__": 1, "ref": {"values": [{"id": 94817815, "src": "hda"}]}, "ref_sel": "history"}

      

      
optimization
"--rna"

      

      
expert_settings
{"evs": {"__current_case__": 1, "indelScoringModelFile": null, "reportEVSFeatures": "false", "selector": "enableEVS", "snvScoringModelFile": null}, "s_e_e": ""}

      

      
regions
{"__current_case__": 0, "restrict_to_region": "genome"}

      

      
forced_regions
[]

      

      
pl
{"callContinuousVf": "Chr1", "ploidy": null}

      

      
oo
{"gvcf": {"__current_case__": 1, "emit_gvcfs": "yes", "noCompress": null}, "vcf_type": "false"}

      

      
strelka
{"maxIndelSize": "51", "minMapq": "21"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"cram"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

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        Mar 26, 2022


      
    


  





      


        


  
    

      
          
/run_tool_test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    











      

  
    

      
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/run_tool_test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    










    

  
      



  

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/run_tool_test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    










    

  
      



  

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/run_tool_test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    














      

  
          

  

    
  


  

      

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          @mvdbeek 
        
          @jennaj