fmriprep: TemplateFlow permissions error in 1.3.0

Relevant traceback:

  File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 621, in init_skullstrip_ants_wf
    t1_skull_strip.inputs.brain_template = get_template(skull_strip_template, 'res-01_T1w.nii.gz')
  File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 24, in get
    out_file = api.get(filepath)
[...]
  File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 530, in run
    raise CommandError(str(cmd), msg, status, out[0], out[1])
datalad.support.exceptions.CommandError: CommandError: command '['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz']' failed with exitcode 1
Failed to run ['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz'] under '/opt/templateflow/tpl-OASIS30ANTs'. Exit code=1. out= err=git-annex: .git/annex/journal.lck: openFd: permission denied (Permission denied)

My suspicion is that the solution would be to add umask 000 before datalad commands in the Dockerfile.

Full log.

cc @Gilles86 @oesteban

About this issue

  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 23 (23 by maintainers)

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