singularity run with pydeface fails due to TraitError from nipype

[yarikoptic]

~/proj/nuisance/data/dbic-deid$ singularity run --cleanenv  envs/bidsonym_latest.sif sourcedata participant --participant_label=sid000003 --deid pydeface
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
This dataset appears to be BIDS compatible.

        Summary:                   Available Tasks:        Available Modalities: 
        1115 Files, 11.56MB                                T1w                   
        206 - Subjects                                                           
        370 - Sessions                                                           


	If you have any questions, please post on https://neurostars.org/tags/bids.

200722-09:29:01,828 nipype.utils INFO:
	 Running nipype version 1.5.0-rc1 (latest: 1.5.0)
200722-09:29:02,281 nipype.workflow INFO:
	 Workflow deface_wf settings: ['check', 'execution', 'logging', 'monitoring']
200722-09:29:02,290 nipype.workflow INFO:
	 Running serially.
200722-09:29:02,291 nipype.workflow INFO:
	 [Node] Setting-up "deface_wf.pydeface" in "/tmp/tmpk8cxi8ex/deface_wf/pydeface".
200722-09:29:02,292 nipype.workflow INFO:
	 [Node] Running "pydeface" ("nipype.interfaces.utility.wrappers.Function")
--------------
pydeface 2.0.0
--------------
Temporary files:
  /tmp/tmpi4i7x5mr.mat
  /tmp/tmplev6753o.nii.gz
Defacing...
  sourcedata/sub-sid000003/ses-XXXXXXXXXXX/anat/sub-sid000003_ses-20161011X092931_T1w.nii.gz
200722-09:29:03,153 nipype.utils INFO:
	 Running nipype version 1.5.0-rc1 (latest: 1.5.0)
Traceback (most recent call last):
  File "/opt/miniconda-latest/envs/bidsonym/bin/pydeface", line 11, in <module>
    load_entry_point('pydeface==2.0.0', 'console_scripts', 'pydeface')()
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/pydeface-2.0.0-py3.6.egg/pydeface/__main__.py", line 95, in main
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/pydeface-2.0.0-py3.6.egg/pydeface/utils.py", line 99, in deface_image
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/traits/base_trait_handler.py", line 77, in error
    object, name, self.full_info(object, name, value), value
traits.trait_errors.TraitError: The 'reference' trait of a FLIRTInputSpec instance must be a pathlike object or string representing an existing file, but a value of 'sourcedata/sub-sid000003/ses-XXXXX/anat/sub-sid000003_ses-XXXXXX_T1w.nii.gz' <class 'str'> was specified.
200722-09:29:03,304 nipype.workflow WARNING:
	 Storing result file without outputs
200722-09:29:03,306 nipype.workflow WARNING:
	 [Node] Error on "deface_wf.pydeface" (/tmp/tmpk8cxi8ex/deface_wf/pydeface)
200722-09:29:03,308 nipype.workflow ERROR:
	 Node pydeface failed to run on host smaug.
200722-09:29:03,309 nipype.workflow ERROR:
	 Saving crash info to /home/chrispycheng/proj/nuisance/data/dbic-deid/crash-20200722-092903-chrispycheng-pydeface-7fc94405-bc25-4fda-a538-a5eb543ee23a.pklz
Traceback (most recent call last):
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
    node.run(updatehash=updatehash)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 397, in run
    runtime = self._run_interface(runtime)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
    out = function_handle(**args)
  File "<string>", line 9, in pydeface_cmd
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/subprocess.py", line 311, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['pydeface', SENSORED by yarik, '--force']' returned non-zero exit status 1.

200722-09:29:03,310 nipype.workflow INFO:
	 ***********************************
200722-09:29:03,310 nipype.workflow ERROR:
	 could not run node: deface_wf.pydeface
200722-09:29:03,310 nipype.workflow INFO:
	 crashfile: /home/chrispycheng/proj/nuisance/data/dbic-deid/crash-20200722-092903-chrispycheng-pydeface-7fc94405-bc25-4fda-a538-a5eb543ee23a.pklz
200722-09:29:03,310 nipype.workflow INFO:
	 ***********************************
Traceback (most recent call last):
  File "/opt/miniconda-latest/envs/bidsonym/bin/bidsonym", line 11, in <module>
    load_entry_point('bidsonym', 'console_scripts', 'bidsonym')()
  File "/home/bm/bidsonym/run_deeid.py", line 111, in run_deeid
    run_pydeface(T1_file, T1_file)
  File "/home/bm/bidsonym/defacing_algorithms.py", line 32, in run_pydeface
    deface_wf.run()
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 70, in run
    report_nodes_not_run(notrun)
  File "/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 98, in report_nodes_not_run
    ("Workflow did not execute cleanly. " "Check log for details")
RuntimeError: Workflow did not execute cleanly. Check log for details

[PeerHerholz]

Hm, not entirely sure what's going wrong here. Could you try again with the latest version?