Unable to run Example 1: Preprocessing Workflow

[avatar-lavventura]

I am trying to run Example 1: Preprocessing Workflow.

I am able to make it work up to this line: preproc.run('MultiProc', plugin_args={'n_procs': 8}).

At that line, I am getting following error, I am not sure why I am getting this error: Please not that I am getting similar error on other examples as well.

181025-14:22:48,815 nipype.workflow INFO:
	 Generated workflow graph: output/workingdir/preproc/graph.png (graph2use=colored, simple_form=True).
181025-14:22:49,260 nipype.workflow INFO:
	 Generated workflow graph: /home/netlab/nipype/tutorial/output/workingdir/preproc/graph.png (graph2use=flat, simple_form=True).
181025-14:22:49,343 nipype.workflow INFO:
	 Workflow preproc settings: ['check', 'execution', 'logging', 'monitoring']
181025-14:22:49,424 nipype.workflow INFO:
	 Running in parallel.
181025-14:22:49,428 nipype.workflow INFO:
	 [MultiProc] Running 0 tasks, and 10 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 8/8.
181025-14:22:49,473 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles".
181025-14:22:49,474 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles".
181025-14:22:49,475 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles".
181025-14:22:49,477 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,477 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles".
181025-14:22:49,478 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles".
181025-14:22:49,479 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles".
181025-14:22:49,480 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,481 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles)
181025-14:22:49,481 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles".
181025-14:22:49,481 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,483 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,484 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles".
181025-14:22:49,484 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,485 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,485 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles)
181025-14:22:49,486 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles)
181025-14:22:49,487 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,488 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles)
181025-14:22:49,489 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:49,490 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles)
181025-14:22:49,490 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles)
181025-14:22:49,492 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles)
181025-14:22:49,493 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles)
181025-14:22:51,436 nipype.workflow ERROR:
	 Node selectfiles.b3 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,437 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b3-94fb1310-d451-4f0a-b902-18fb423287b3.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz

181025-14:22:51,442 nipype.workflow ERROR:
	 Node selectfiles.b4 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,442 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b4-3bb336d6-42c0-41ca-8d11-806c666f4150.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz

181025-14:22:51,447 nipype.workflow ERROR:
	 Node selectfiles.b9 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,447 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b9-9c7ba1ae-5d70-4244-a8ef-25833941d497.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz

181025-14:22:51,452 nipype.workflow ERROR:
	 Node selectfiles.b5 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,452 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b5-8ece5934-dfdb-4dec-a032-008e1b07de2f.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz

181025-14:22:51,457 nipype.workflow ERROR:
	 Node selectfiles.b0 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,457 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b0-904b14da-84c5-4993-90d0-441158f115b0.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz

181025-14:22:51,462 nipype.workflow ERROR:
	 Node selectfiles.b2 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,462 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b2-69b38441-6286-4b89-b195-dfe65605e91c.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz

181025-14:22:51,467 nipype.workflow ERROR:
	 Node selectfiles.b7 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,467 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b7-e7c4179b-b8c1-4c1f-bef5-1a31c4974c52.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz

181025-14:22:51,472 nipype.workflow ERROR:
	 Node selectfiles.b6 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:51,472 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b6-84ff86d7-70f9-4d91-a0fa-037f79658b84.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz

181025-14:22:51,475 nipype.workflow INFO:
	 [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 8/8.
181025-14:22:51,515 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles".
181025-14:22:51,515 nipype.workflow INFO:
	 [Node] Setting-up "preproc.selectfiles" in "/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles".
181025-14:22:51,518 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:51,518 nipype.workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
181025-14:22:51,520 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles)
181025-14:22:51,521 nipype.workflow WARNING:
	 [Node] Error on "preproc.selectfiles" (/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles)
181025-14:22:53,438 nipype.workflow ERROR:
	 Node selectfiles.b8 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:53,439 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142253-netlab-selectfiles.b8-3692bf57-6b47-42de-92b1-b56da02151fe.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz

181025-14:22:53,445 nipype.workflow ERROR:
	 Node selectfiles.b1 failed to run on host sametaytac-HP-Z240-Tower-Workstation.
181025-14:22:53,445 nipype.workflow ERROR:
	 Saving crash info to /home/netlab/nipype/tutorial/crash-20181025-142253-netlab-selectfiles.b1-d0b66d7d-8ea4-4d70-bbb6-608c1b16dc38.pklz
Traceback (most recent call last):
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 524, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/interfaces/io.py", line 1424, in _list_outputs
    raise IOError(msg)
IOError: No files were found matching anat template: /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz

181025-14:22:53,449 nipype.workflow INFO:
	 [MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 8/8.
181025-14:22:55,433 nipype.workflow INFO:
	 ***********************************
181025-14:22:55,433 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b3
181025-14:22:55,433 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b3-94fb1310-d451-4f0a-b902-18fb423287b3.pklz
181025-14:22:55,434 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b4
181025-14:22:55,434 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b4-3bb336d6-42c0-41ca-8d11-806c666f4150.pklz
181025-14:22:55,434 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b9
181025-14:22:55,434 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b9-9c7ba1ae-5d70-4244-a8ef-25833941d497.pklz
181025-14:22:55,434 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b5
181025-14:22:55,434 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b5-8ece5934-dfdb-4dec-a032-008e1b07de2f.pklz
181025-14:22:55,434 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b0
181025-14:22:55,435 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b0-904b14da-84c5-4993-90d0-441158f115b0.pklz
181025-14:22:55,435 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b2
181025-14:22:55,435 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b2-69b38441-6286-4b89-b195-dfe65605e91c.pklz
181025-14:22:55,435 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b7
181025-14:22:55,435 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b7-e7c4179b-b8c1-4c1f-bef5-1a31c4974c52.pklz
181025-14:22:55,435 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b6
181025-14:22:55,435 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142251-netlab-selectfiles.b6-84ff86d7-70f9-4d91-a0fa-037f79658b84.pklz
181025-14:22:55,436 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b8
181025-14:22:55,436 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142253-netlab-selectfiles.b8-3692bf57-6b47-42de-92b1-b56da02151fe.pklz
181025-14:22:55,436 nipype.workflow ERROR:
	 could not run node: preproc.selectfiles.b1
181025-14:22:55,436 nipype.workflow INFO:
	 crashfile: /home/netlab/nipype/tutorial/crash-20181025-142253-netlab-selectfiles.b1-d0b66d7d-8ea4-4d70-bbb6-608c1b16dc38.pklz
181025-14:22:55,436 nipype.workflow INFO:
	 ***********************************
Traceback (most recent call last):
  File "run.py", line 206, in <module>
    preproc.run('MultiProc', plugin_args={'n_procs': 8})
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 192, in run
    report_nodes_not_run(notrun)
  File "/home/netlab/.local/lib/python2.7/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[miykael]

That it crashes when you want to run the workflow means that the workflow itself is ok (i.e. the connections are all valid), but that something happend during the execution.

At the end of the log you have a section that is enclosed by *********************************** and there it tells you that the crashfile has something to do with selectfiles. Now if you go just above the first ***********************************, you will find the actual error messages:

IOError: No files were found matching anat template:
/home/netlab/nipype/tutorial/output/workingdir/preproc/
    _subject_id_02_task_name_fingerfootlips/selectfiles/data/ds000114/
    derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz

This means that the selectfiles folder cannot find the input files. Can you verify that the files are at this location?

[avatar-lavventura]

I guess the required file is not created during executing. Any of the preproc/_subject_id_02_task_name_fingerfootlips/selectfiles folder does not contain data folder.

$ ls /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_0*_task_name_fingerfootlips/selectfiles/
/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

/home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles/:
crashstore.pklz  _inputs.pklz  _node.pklz  _report

$ cat /home/netlab/nipype/tutorial/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz
cat: /home/netlab/...data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz: No such file or directory

[miykael]

The input shouldn't be created. Those paths should lead to the actual files on your system.

Make sure that the base_directory path of selectfiles points to your data:

selectfiles = Node(SelectFiles(templates,
                               base_directory='/data/ds000114'),
                   name="selectfiles")

Also, make sure that base_dir of the workflow is an absolute path:

preproc = Workflow(name='preproc')
preproc.base_dir = '/home/netlab/nipype/tutorial/

[avatar-lavventura]

netlab@TETAM:~/nipype/tutorial$ pwd
/home/netlab/nipype/tutorial
netlab@TETAM:~/nipype/tutorial$ ls
data  run.py

preproc.base_dir = opj(experiment_dir, working_dir) => preproc.base_dir was output/workingdir. I set it to /home/netlab/nipype/tutorial.

---

I have set full path for base_directory as well.

selectfiles = Node(SelectFiles(templates,
              base_directory='/home/netlab/nipype/tutorial/data/ds000114'),
              name="selectfiles")

---

Later I get following error for many function calls: UnicodeEncodeError: 'utf-8' codec can't encode characters in position 4727-4728: surrogates not allowed for Python2.7 and Python3.5.

Please see error log.

[miykael]

Hmm.. So, it got further but broke again. Not sure, but there seems to be an issue with a character in the filename. Could you also share the content of _report/report.txt in the selectfiles folder? (And thanks for the error log in gist 👍)

[avatar-lavventura]

I guess since it's broken at different point, it does not generate any output folder under /home/netlab/nipype/tutorial/ anymore.

[miykael]

This should be in your workingdir. Or in your case it might be under /home/netlab/nipype/tutorial/preproc. Also, how big is your data folder, i.e. can you open the input image that you try to use as input?

It's sometimes confusing with datalad the files seem to be there but are actually only links/references to files.