nipype.workflow WARNING and ERROR when attempting to run MRIQC using singularity

Hello,

I am attempting to run mriqc on T1w and T2w data on a secure cluster using a singularity image. When doing so I get nipype.workflow related warnings and errors which I were unable to successfully troubleshoot. Any input on what I might be doing wrong would be greatly appreciated!

Kind regards Linn Bonaventure

Code:

#!/bin/bash
#SBATCH --job-name=mriqc_step1
#SBATCH --account= abc
#SBATCH --time=04:00:00
#SBATCH --mem-per-cpu=20GB
#SBATCH --output="xyz/logs/slurm.%j.out"
#SBATCH --array=1-2%2 

#load modules
module load singularity/3.7

echo "setting paths"
#set paths
MRIQC_dir="/xyz/lcnorbom/mriqc"
BIDS_dir="/xyz/lcnorbom/testing_POND"
SUBJECT_LIST="/xyz/lcnorbom/docs/n2_subjids_testing_POND.txt"

subject=$( sed "${SLURM_ARRAY_TASK_ID}q;d" ${SUBJECT_LIST})

echo "uploading bids"
#copy relevant subject from BIDS_directory to a holding folder 
cp -r ${BIDS_dir}/$subject ${MRIQC_dir}/for_holding_bids_new/

#MRIQC step1 command
#obs testing only on T1w data for now
cmd="singularity run --cleanenv -B ${MRIQC_dir}/for_holding_bids_new:/data -B ${MRIQC_dir}/out:/out -B ${SLURM_TMPDIR}:/work  /xyz/lcnorbom/SOFTWARE/mriqc_alt2.simg /data /out participant --participant-label $subject --no-sub -w /work -m T1w"

echo Running task ${SLURM_ARRAY_TASK_ID}
echo Commandline: $cmd
eval $cmd
exitcode=$?

Copy of slurm log:

setting paths
uploading bids
Running task 1
Commandline: singularity run --cleanenv -B /xyz/lcnorbom/mriqc/for_holding_bids_new:/data -B /xyz/lcnorbom/mriqc/out:/out -B /localscratch/lcnorbom.65875485.0:/work /xyz/lcnorbom/SOFTWARE/mriqc_alt2.simg /data /out participant --participant-label sub-0880498 --no-sub -w /work -m T1w
221004-10:58:30,591 cli IMPORTANT:

    Running MRIQC version 22.0.6:
      * BIDS dataset path: /data.
      * Output folder: /out.
      * Analysis levels: ['participant'].

Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
221004-11:09:29,832 nipype.workflow WARNING:
     Storing result file without outputs
221004-11:09:29,844 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.SpatialNormalization.SpatialNormalization" (/work/mriqc_wf/anatMRIQC/SpatialNormalization/_in_file_..data..sub-0880498..ses-01..anat..sub-0880498_ses-01_T1w.nii.gz/SpatialNormalization)
221004-11:09:30,513 nipype.workflow ERROR:
     Node SpatialNormalization.a0 failed to run on host gra809.
221004-11:09:30,514 nipype.workflow ERROR:
     Saving crash info to /out/logs/crash-20221004-110930-lcnorbom-SpatialNormalization.a0-51deb0d3-bc36-465a-9400-949f439f069c.txt

nipreps / mriqc

nipype.workflow WARNING and ERROR when attempting to run MRIQC using singularity #1031