We have set up fmriprep (1.3.2) in a singularity (3.4.0) container on our grid cluster (CentOS 6.3). If I connect directly to one of our nodes and run my singularity-fmriprep command, the pipeline will run to completion. However, when I pass the command to a node with qsub, fmriprep begins, does the BIDS validation, generates the boilerplate, and stops without errors. We haven’t been able to figure out why this would be happening. Does anyone have similar experiences, or things they suggest we look into? Thank you!
Command and outputs below:
This is my singularity-fmriprep command:
singularity run --cleanenv --bind /data:/mnt /opt/fmriprep-1.3.2 /mnt/chen_lab/jmatthews/GridNodeTest/input/ds002156-1.0.0/ /mnt/chen_lab/jmatthews/GridNodeTest/output/ participant -w /mnt/chen_lab/jmatthews/fmriprep-work/ --fs-license-file /mnt/chen_lab/jmatthews/fmriprep-work/license.txt
This command is saved in a file named “fmriprep_command_long” and passed with command:
qsub -cwd fmriprep_command_long
The resulting qsub files are:
-which is empty
-which contains (I have condensed this output with ellipses, as it is long and the outputs contain “@” symbols which the forum is flagging as user tags, and I don’t know how to get around. If I’m missing anything critical, please ask.):
This dataset appears to be BIDS compatible.
If you have any questions please post on https://neurostars.org/tags/bids
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
191022-15:50:00,673 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.3.2: * BIDS dataset path: /mnt/chen_lab/jmatthews/GridNodeTest/input/ds002156-1.0.0. * Participant list: ['23638']. * Run identifier: 20191022-155000_9cac8d1e-745d-471d-90a7-12f82ede0cc1.
Works derived from this fMRIPrep execution should include the following boilerplate:
Anatomical data preprocessing
Functional data preprocessing
Many internal operations of fMRIPrep use