Manta crash during getDepthFromAlignments
0
0
Entering edit mode
20 days ago

I'm running Manta as part of a Nextflow pipeline in the Seqera platform, and I'm seeing this when runWorkflow.py runs. Appreciate any help in resolving this.

  Failed to complete master workflow, error code: 1
  errorMessage:
  Unhandled Exception in TaskRunner-Thread-masterWorkflow
  Traceback (most recent call last):
    File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1069, in run
      (retval, retmsg) = self._run()
    File "/usr/local/share/manta-1.6.0-1/lib/python/pyflow/pyflow.py", line 1121, in _run
      self.workflow.workflow()
    File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 850, in workflow
      depthTasks = mantaGetDepthFromAlignments(self)
    File "/usr/local/share/manta-1.6.0-1/lib/python/mantaWorkflow.py", line 237, in mantaGetDepthFromAlignments
      return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
    File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 194, in getDepthFromAlignments
      return _getDepthShared(self, taskPrefix, dependencies, bamList, outputPath, depthFunc)
    File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 113, in _getDepthShared
      scatterTasks |= setzer(depthFunc(self,taskPrefix+"_sample"+indexStr,dirTask,bamFile,tmpFiles[-1]))
    File "/usr/local/share/manta-1.6.0-1/lib/python/sharedWorkflow.py", line 184, in depthFunc
      assert(len(tmpFiles) != 0)
  AssertionError
manta sv • 123 views
ADD COMMENT

Login before adding your answer.

Traffic: 5713 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6