nipy/nipype — Issue #319: dmri_group_connectivity_camino.py crashes
Author: chrisfilo
Created: 2012-03-03 12:58:22+00:00
State: open

DEBUG:workflow:(l3output.l3infosource, l3output.l3source): No edge data
DEBUG:workflow:(l3output.l3infosource, l3output.l3source): new edge data: {'connect': [('group_id', 'group_id')]}
DEBUG:workflow:(l3output.l3source, l3output.l3inputnode): No edge data
DEBUG:workflow:(l3output.l3source, l3output.l3inputnode): new edge data: {'connect': [('CFFfiles', 'Group_CFFs')]}
DEBUG:workflow:(l3output.l3inputnode, l3output.MergeCNetworks_grp): No edge data
DEBUG:workflow:(l3output.l3inputnode, l3output.MergeCNetworks_grp): new edge data: {'connect': [('Group_CFFs', 'in_files')]}
DEBUG:workflow:(l3output.MergeCNetworks_grp, l3output.l3datasink): No edge data
DEBUG:workflow:(l3output.MergeCNetworks_grp, l3output.l3datasink): new edge data: {'connect': [('connectome_file', '@l3output')]}
DEBUG:workflow:Creating flat graph for workflow: l3output
DEBUG:workflow:expanding workflow: l3output
DEBUG:workflow:processing node: l3output.l3infosource
DEBUG:workflow:processing node: l3output.l3source
DEBUG:workflow:processing node: l3output.l3inputnode
DEBUG:workflow:processing node: l3output.MergeCNetworks_grp
DEBUG:workflow:processing node: l3output.l3datasink
DEBUG:workflow:finished expanding workflow: l3output
INFO:workflow:['execution', 'logging']
DEBUG:workflow:PE: expanding iterables
DEBUG:workflow:setting nodelevel(l3output.l3source) input group_id = ['parkinsons', 'controls']
DEBUG:workflow:PE: expanding iterables ... done
INFO:workflow:Running in parallel.
INFO:workflow:Submitting 1 jobs
INFO:workflow:Executing: l3source ID: 1 H:c5ad6c34cc925df1bde23767558f4cd8
DEBUG:workflow:checking hash locally
DEBUG:workflow:Hash exists False
DEBUG:workflow:Finished checking hash True
DEBUG:workflow:Setting node inputs
INFO:workflow:Executing node l3source in dir: /mnt/data/nipype_examples/dmri_group_connectivity_camino/l3output/l3source
DEBUG:workflow:Node hash: c5ad6c34cc925df1bde23767558f4cd8
DEBUG:workflow:Removing old /mnt/data/nipype_examples/dmri_group_connectivity_camino/l3output/l3source and its contents
DEBUG:workflow:Creating /mnt/data/nipype_examples/dmri_group_connectivity_camino/l3output/l3source
DEBUG:workflow:writing pre-exec report to /mnt/data/nipype_examples/dmri_group_connectivity_camino/l3output/l3source/_report/report.rst
DEBUG:workflow:Executing node
DEBUG:workflow:copying files to wd [execute=True, linksonly=False]
ERROR:workflow:['Node l3source failed to run on host filolaptop.']
INFO:workflow:Saving crash info to /mnt/data/nipype_examples/crash-20120303-124711-filo-l3source.npz
INFO:workflow:Traceback (most recent call last):
File "/home/filo/workspace/nipype/nipype/pipeline/plugins/multiproc.py", line 15, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/home/filo/workspace/nipype/nipype/pipeline/engine.py", line 1125, in run
self._run_interface()
File "/home/filo/workspace/nipype/nipype/pipeline/engine.py", line 1220, in _run_interface
self._result = self._run_command(execute)
File "/home/filo/workspace/nipype/nipype/pipeline/engine.py", line 1344, in _run_command
result = self._interface.run()
File "/home/filo/workspace/nipype/nipype/interfaces/base.py", line 824, in run
results.outputs = self.aggregate_outputs(results.runtime)
File "/home/filo/workspace/nipype/nipype/interfaces/base.py", line 866, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/home/filo/workspace/nipype/nipype/interfaces/io.py", line 509, in _list_outputs
raise IOError(msg)
IOError: Output key: CFFfiles Template: /mnt/data/nipype_examples/dmri_group_connectivity_camino/parkinsons/parkinsons.cff returned no files
Interface DataGrabber failed to run. Inputs:
base_directory =
field_template =
group_id = ['parkinsons', 'controls']
ignore_exception = False
raise_on_empty = True
sort_filelist = False
template = /mnt/data/nipype_examples/dmri_group_connectivity_camino/%s/%s.cff
template_args = {'CFFfiles': [['group_id', 'group_id']]}

INFO:workflow:***********************************
ERROR:workflow:could not run node: l3output.l3source
INFO:workflow:crashfile: /mnt/data/nipype_examples/crash-20120303-124711-filo-l3source.npz
DEBUG:workflow:The following dependent nodes were not run
DEBUG:workflow:l3source
DEBUG:workflow:MergeCNetworks_grp
DEBUG:workflow:l3datasink
INFO:workflow:***********************************
Traceback (most recent call last):
File "/home/filo/workspace/nipype/examples/dmri_group_connectivity_camino.py", line 168, in
l3pipeline.run()
File "/home/filo/workspace/nipype/nipype/pipeline/engine.py", line 520, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/home/filo/workspace/nipype/nipype/pipeline/plugins/base.py", line 182, in run
report_nodes_not_run(notrun)
File "/home/filo/workspace/nipype/nipype/pipeline/plugins/base.py", line 87, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

Please also make sure that dmri_group_connectivity_mrtrix.py runs cleanly