Manta crash during getDepthFromAlignments

Question

[lucas.lochovsky]

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