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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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AssertionError: assert len(genomeNodes) == 1 #125

Open Jome0169 opened 3 years ago

Jome0169 commented 3 years ago

Hello,

I've been using progressive cactus to great effect, but recently hit an error as I increased the number of genomes I was analyzing. The error is as follows:

    [2021-03-18T15:49:28-0400] [MainThread] [I] [cactus.progressive.cactus_progressive] Sequences in progressive, 0.859673: ['oryza_sativa', 'setaria_virdis']

Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/toil/worker.py", line 368, in workerScript job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/usr/local/lib/python3.6/dist-packages/cactus/shared/common.py", line 1369, in _runner super(RoundedJob, self)._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/usr/local/lib/python3.6/dist-packages/toil/job.py", line 1424, in _runner returnValues = self._run(jobGraph, fileStore) File "/usr/local/lib/python3.6/dist-packages/toil/job.py", line 1361, in _run return self.run(fileStore) File "/usr/local/lib/python3.6/dist-packages/cactus/progressive/cactus_progressive.py", line 189, in run workFlowArgs = CactusWorkflowArguments(self.options, experimentFile=experimentFile, configNode=configNode, seqIDMap = seqIDMap) File "/usr/local/lib/python3.6/dist-packages/cactus/pipeline/cactus_workflow.py", line 1378, in init self.experimentWrapper.setSequenceID(genome, seqID) File "/usr/local/lib/python3.6/dist-packages/cactus/shared/experimentWrapper.py", line 354, in setSequenceID assert len(genomeNodes) == 1 AssertionError [2021-03-18T15:49:28-0400] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host d1-21.compute.lan ('setting this', 'oryza_sativa', 'files/for-job/kind-MergeChunks2/instance-plun6ik2/file-yapyul9z/tmpwyjui_uf.tmp')

with the taceback looking like...

Traceback (most recent call last):
  File "/usr/local/bin/cactus", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/dist-packages/cactus/progressive/cactus_progressive.py", line 386, in main
    runCactusProgressive(options)
  File "/usr/local/lib/python3.6/dist-packages/cactus/progressive/cactus_progressive.py", line 434, in runCactusProgressive
    halID = toil.start(RunCactusPreprocessorThenProgressiveDown(options, project, memory=configWrapper.getDefaultMemory()))
  File "/usr/local/lib/python3.6/dist-packages/toil/common.py", line 846, in start
    return self._runMainLoop(rootJobGraph)
  File "/usr/local/lib/python3.6/dist-packages/toil/common.py", line 1138, in _runMainLoop
    jobCache=self._jobCache).run()
  File "/usr/local/lib/python3.6/dist-packages/toil/leader.py", line 235, in run
    self.innerLoop()
  File "/usr/local/lib/python3.6/dist-packages/toil/leader.py", line 567, in innerLoop
    self._gatherUpdatedJobs(updatedJobTuple)
  File "/usr/local/lib/python3.6/dist-packages/toil/leader.py", line 527, in _gatherUpdatedJobs
    self.processFinishedJob(jobID, exitStatus, wallTime=wallTime, exitReason=exitReason)
  File "/usr/local/lib/python3.6/dist-packages/toil/leader.py", line 920, in processFinishedJob
    StatsAndLogging.writeLogFiles(jobGraph.chainedJobs, logFileStream, self.config, failed=True)
  File "/usr/local/lib/python3.6/dist-packages/toil/statsAndLogging.py", line 132, in writeLogFiles
    with writeFn(fullName, 'wb') as f:

I'm unsure what could be generating this error as both genomes input into Cactus are formatted correctly. Any ideas would be greatly appreciated.