Open
Description
What happened?
Popped up in the CI.
Specifically, a crash occurs:
240831-21:10:41,685 nipype.workflow WARNING:
[Node] Error on "nibabies_24_1_wf.fsdir_run_20240831_211035_585ba987_6362_4fdc_adf4_96fbcefd71f4" (/scratch/nibabies_24_1_wf/fsdir_run_20240831_211035_585ba987_6362_4fdc_adf4_96fbcefd71f4)
240831-21:10:41,686 nipype.workflow ERROR:
Node fsdir_run_20240831_211035_585ba987_6362_4fdc_adf4_96fbcefd71f4 failed to run on host b68c6b836a11.
240831-21:10:41,686 nipype.workflow ERROR:
Saving crash info to /out/logs/crash-20240831-211041-UID1001-fsdir_run_20240831_211035_585ba987_6362_4fdc_adf4_96fbcefd71f4-e569a10e-8616-4885-b226-b83db48dbfed.txt
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node fsdir_run_20240831_211035_585ba987_6362_4fdc_adf4_96fbcefd71f4.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/niworkflows/interfaces/bids.py", line 1475, in _run_interface
shutil.copytree(source, dest, copy_function=shutil.copy)
File "/opt/conda/envs/nibabies/lib/python3.11/shutil.py", line 573, in copytree
return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/shutil.py", line 471, in _copytree
os.makedirs(dst, exist_ok=dirs_exist_ok)
File "<frozen os>", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/opt/subjects/fsaverage'
yet the log ends with
240831-21:19:39,613 nipype.workflow IMPORTANT:
nibabies finished successfully!
240831-21:19:39,613 nipype.workflow IMPORTANT:
Works derived from this nibabies execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
What command did you use?
docker run --rm -e DOCKER_VERSION_8395080871=26.0.2 -it -u 1001:1002 --network=none -e NIBABIES_DEV=1 -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro -v /tmp/data/bcp:/data:ro -v /tmp/bcp/derivatives/nibabies:/out -v /tmp/data/bcp/derivatives/infant-freesurfer:/opt/subjects -v /tmp/data/bcp/derivatives/bibsnet:/deriv/precomputed:ro -v /tmp/bcp/work:/scratch -v opts.config:/home/fmriprep/.nipype/nipype.cfg:ro nipreps/nibabies:dev /data /out participant --notrack --skull-strip-template UNCInfant:cohort-1 --sloppy --write-graph --mem-mb 14000 --nthreads 4 -vv --age-months 2 --sloppy --surface-recon-method infantfs --output-layout bids --anat-only --fs-subjects-dir /opt/subjects --derivatives precomputed=/deriv/precomputed -w /scratch --output-spaces MNIInfant:cohort-1 funcWhat version of NiBabies are you using?
24.0.1
Relevant log output
No response
Add any additional information or context about the problem here.
No response