Summary of what happened:
I am trying to run fmriprep for the first time and have ran into an error which seems due to issues with writing certain files (althoguh some other files have been written with no issues?). An example of the error is below.
Thank you very much!
Command used (and if a helper script was used, a link to the helper script or the command generated):
Version:
Environment (Docker, Singularity, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 328, in _invoke_callbacks
callback(self)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
result = args.result()
File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 437, in result
return self.__get_result()
File "/opt/conda/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result
raise self._exception
FileNotFoundError: /mypath/data/work/fmriprep/fmriprep_wf/single_subject_220751_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/result__midthickness1.pklz
221217-06:56:35,520 nipype.workflow WARNING:
[Node] Error on "_midthickness0" (/mypath/fmriprep/fmriprep_wf/single_subject_220751_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0)
exception calling callback for <Future at 0x7fae877a7d30 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 758, in _run_command
result.outputs = clean_working_directory(
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/utils.py", line 1524, in clean_working_directory
os.remove(f)
PermissionError: [Errno 13] Permission denied: '/mypath/data/work/fmriprep/fmriprep_wf/single_subject_220751_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.smoothwm'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 70, in run_node
result["result"] = node.result
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 216, in result
return _load_resultfile(
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/utils.py", line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /mypath/data/work/fmriprep/fmriprep_wf/single_subject_220751_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/result__midthickness0.pklz