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.
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 23 (23 by maintainers)
Commits related to this issue
- BF: set annex.merge-annex-branches=false for invocations not requiring updated remote information git-annex pretty much for any command which could potentially benefit from updated availability infor... — committed to yarikoptic/datalad by yarikoptic 5 years ago
- BF: set annex.merge-annex-branches=false for invocations not requiring updated remote information git-annex pretty much for any command which could potentially benefit from updated availability infor... — committed to yarikoptic/datalad by yarikoptic 5 years ago
- BF: set annex.merge-annex-branches=false for invocations not requiring updated remote information pretty much for any command which could potentially benefit from updated availability information pre... — committed to yarikoptic/datalad by yarikoptic 5 years ago
fix on datalad side is WiP: https://github.com/datalad/datalad/pull/3164