Illumina/manta

Error: Unhandled Exception in TaskRunner-Thread-masterWorkflow

georgiesamaha opened this issue · 1 comments

georgiesamaha commented

Hello,

I'm receiving a pyflow error when running Manta with Singularity. My command is:

manta=docker://quay.io/biocontainers/manta:1.6.0--h9ee0642_1
refDir=/data/Reference
bamDir=/data/Bams
workDir=~/Germline-StructuralV-nf
bam=${bamDir}/MYUM011_sorted.bam
ref=${refDir}/hg38.fa
manta_bed=${refDir}/HG38_manta_include.bed.gz
cpus=4

singularity exec -B ${bamDir} -B ${refDir} ${manta} \
configManta.py \
	--normalBam ${bam} \
	--referenceFasta ${ref} \
	--runDir manta \
	--callRegions $manta_bed 

singularity exec -B ${bamDir} -B ${refDir} -B ${workDir} ${manta} \
	manta/runWorkflow.py -j ${cpus}

Output log is

INFO:    Using cached SIF image
[2022-09-16T05:21:10.224103Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Initiating pyFlow run
[2022-09-16T05:21:10.345593Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2022-09-16T05:21:10.442598Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2022-09-16T05:21:10.512673Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2022-09-16T05:21:10.549392Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] WorkingDir: '/home/ubuntu/Germline-StructuralV-nf/testScripts'
[2022-09-16T05:21:10.616744Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] ProcessCmdLine: '/home/ubuntu/Germline-StructuralV-nf/testScripts/manta/runWorkflow.py -j 4'
[2022-09-16T05:21:10.674247Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] mode: local
[2022-09-16T05:21:10.794105Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] nCores: 4
[2022-09-16T05:21:10.821678Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] memMb: 257747
[2022-09-16T05:21:10.825270Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] dataDir: /home/ubuntu/Germline-StructuralV-nf/testScripts/manta/workspace/pyflow.data
[2022-09-16T05:21:10.914469Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2022-09-16T05:21:11.056067Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] isContinue: False
[2022-09-16T05:21:11.115413Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2022-09-16T05:21:11.213116Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2022-09-16T05:21:11.319764Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2022-09-16T05:21:11.380814Z] [sv-analysis.novalocal] [3950628_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2022-09-16T05:21:11.519049Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2022-09-16T05:21:11.653309Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2022-09-16T05:21:11.761805Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2022-09-16T05:21:11.765828Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2022-09-16T05:21:11.834952Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2022-09-16T05:21:11.994758Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2022-09-16T05:21:12.117668Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2022-09-16T05:21:12.238101Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getChromDepth_makeTmpDir' to master workflow
[2022-09-16T05:21:12.436463Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] Adding command task 'getChromDepth_sample000_makeTmpDir' to master workflow
[2022-09-16T05:21:12.830319Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getChromDepth_makeTmpDir' from master workflow
[2022-09-16T05:21:12.972852Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2022-09-16T05:21:13.027493Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getChromDepth_makeTmpDir] Task initiated on local node
[2022-09-16T05:21:13.194980Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2022-09-16T05:21:13.379160Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2022-09-16T05:21:13.741317Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getChromDepth_makeTmpDir' launched from master workflow
[2022-09-16T05:21:13.745732Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getChromDepth_sample000_makeTmpDir' from master workflow
[2022-09-16T05:21:13.761898Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getChromDepth_sample000_makeTmpDir] Task initiated on local node
[2022-09-16T05:21:14.525431Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getChromDepth_sample000_makeTmpDir' launched from master workflow
[2022-09-16T05:21:28.930757Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2022-09-16T05:21:28.935414Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2022-09-16T05:21:28.943344Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2022-09-16T05:21:29.305580Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2022-09-16T05:21:29.371198Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2022-09-16T05:21:29.441693Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2022-09-16T05:21:29.510465Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2022-09-16T05:21:29.625576Z] [sv-analysis.novalocal] [3950628_1] [TaskRunner:summarizeStats] Task initiated on local node
[2022-09-16T05:21:30.326772Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2022-09-16T05:21:30.476213Z] [sv-analysis.novalocal] [3950628_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2022-09-16T05:21:30.543457Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR] Failed to complete master workflow, error code: 1
[2022-09-16T05:21:30.693782Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR] errorMessage:
[2022-09-16T05:21:30.700795Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR] Unhandled Exception in TaskRunner-Thread-masterWorkflow
[2022-09-16T05:21:30.707218Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR] Traceback (most recent call last):
[2022-09-16T05:21:30.713721Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1069, in run
[2022-09-16T05:21:30.719408Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     (retval, retmsg) = self._run()
[2022-09-16T05:21:30.726016Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1121, in _run
[2022-09-16T05:21:30.732534Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     self.workflow.workflow()
[2022-09-16T05:21:30.739340Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 850, in workflow
[2022-09-16T05:21:30.756866Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     depthTasks = mantaGetDepthFromAlignments(self)
[2022-09-16T05:21:30.764416Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 237, in mantaGetDepthFromAlignments
[2022-09-16T05:21:30.770165Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
[2022-09-16T05:21:30.776094Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 194, in getDepthFromAlignments
[2022-09-16T05:21:30.782293Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     return _getDepthShared(self, taskPrefix, dependencies, bamList, outputPath, depthFunc)
[2022-09-16T05:21:30.787255Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 113, in _getDepthShared
[2022-09-16T05:21:30.792200Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     scatterTasks |= setzer(depthFunc(self,taskPrefix+"_sample"+indexStr,dirTask,bamFile,tmpFiles[-1]))
[2022-09-16T05:21:30.806875Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]   File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 184, in depthFunc
[2022-09-16T05:21:30.812268Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR]     assert(len(tmpFiles) != 0)
[2022-09-16T05:21:30.817534Z] [sv-analysis.novalocal] [3950628_1] [WorkflowRunner] [ERROR] AssertionError

It might be worth mentioning, I have successfully run this same container and commands on a different system without error. Not sure how to proceed. I have tracked down a related issue which mentions a potential issue with the filesystem I'm working on. Would appreciate any advice on how to proceed.

Cheers,
Georgie

georgiesamaha commented

Resolved this, was a mistake on my part. For those who come across the same issue- I was working with a subset bam file which didn't contain all sequences specified in the --callRegions bed file. The error Manta prints is not descriptive.