Dear all,
I am running fmriprep with singularity:
> #!/bin/sh
> #
> #SBATCH --job-name psy-bkeeser_fmriprep
> #SBATCH --nodes=1
> #SBATCH --ntasks=1
> #SBATCH --cpus-per-task=16
> #SBATCH --mem=32GB
> #SBATCH --output /projects/core-psy/logs/nako/stephan/slurm-%j.log
> #SBATCH --error /projects/core-psy/logs/nako/stephan/slurm-%j.err
>
> singularity run --pwd /tmp3 \
> --home /projects/core-psy/tmp3:/home/fmriprep \
> --cleanenv \
> -B /projects/core-psy/data/nako/swunderl/pa/BIDS_DATA/:/input \
> -B /projects/core-psy/data/nako/bkeeser/test:/output \
> -B /projects/core-psy/data/nako/bkeeser/freesurfer:/freesurfer \
> -B /projects/core-psy/tmp:/opt/templateflow \
> /projects/core-psy/images/nipreps-fmriprep-21.0.1.simg /input /output participant \
> --fs-license-file /freesurfer/license.txt \
> --skip-bids-validation \
> --fs-no-reconall \
which leads to the followng error:
Do I have to mount the tmp folder as well?
> Traceback (most recent call last):
> File "/opt/conda/lib/python3.8/pathlib.py", line 1288, in mkdir
> self._accessor.mkdir(self, mode)
> FileNotFoundError: [Errno 2] No such file or directory: '/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4/bids_db'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/opt/conda/bin/fmriprep", line 8, in <module>
> sys.exit(main())
> File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py", line 38,
> in main parse_args() File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.py", line 679, in parse_args config.from_dict(vars(opts)) File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 666, in from_dict execution.load(settings) File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 238, in load cls.init() File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 465, in init _db_path.mkdir(exist_ok=True, parents=True) File "/opt/conda/lib/python3.8/pathlib.py", line 1292, in mkdir self.parent.mkdir(parents=True, exist_ok=True) File "/opt/conda/lib/python3.8/pathlib.py", line 1288, in mkdir self._accessor.mkdir(self, mode) PermissionError: [Errno 13] Permission denied: '/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4'