Entering edit mode
20 days ago
lucas.lochovsky
•
0
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