Failed with "Read-only file system"

Software Support
1

Summary of what happened:

Hi, I’m trying to run the tractoflow pipeline for one subject on an HPC. The process starts properly, but fails after a few minutes at the Normalize_DWI stage. When looking into the command.log file in the corresponding directory, it seems to be related to a read/write issue. Do you know how this type of error might happen, given that the other steps worked so far?

Thanks,
David

Command used (and if a helper script was used, a link to the helper script or the command generated):

#!/bin/bash
#SBATCH --job-name=tractoflow
#SBATCH --output=logs_nobackup/%j.out
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=8G
#SBATCH --time=24:00:00
#SBATCH --qos=1day

ml Java/8u212b03
./nextflow-21.10.6-all \
    run tractoflow -r 2.4.3 \
    --bids tractoflow/bids \
    -with-singularity scilus_1.6.0.sif \
    -w work_nobackup \
    --output_dir tractoflow/results \
    -resume

Version:

2.4.3

Environment (Docker, Singularity / Apptainer, custom installation):

Nextflow with Singularity Container

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

dwinormalise: [ERROR] dwiextract /scratch/coynel/slurm-job.38181221/nxf.7EZgxsW5wL/sub-1500__dwi_cropped.nii.gz -fslgrad /scratch/coynel/slurm-job.38181221/nxf.7EZgxsW5wL/sub-1500__dwi_eddy_corrected.bvec /scratch/coynel/slurm-job.38181221/nxf.7EZgxsW5wL/sub-1500__bval_eddy -bzero - | mrmath - mean - -axis 3 | mrstats - -mask /scratch/coynel/slurm-job.38181221/nxf.7EZgxsW5wL/sub-1500_fa_wm_mask.nii.gz -output median (individual.py:66)
dwinormalise: [ERROR] Information from failed command:
dwinormalise:
              dwiextract: uncompressing image "/scratch/coynel/slurm-job.38181221/nxf.7EZgxsW5wL/sub-1500__dwi_cropped.nii.gz"... [==================================================]
              dwiextract: [ERROR] error creating temporary file in directory "/scratch/coynel/slurm-job.38181221": Read-only file system
              dwiextract: [ERROR] error creating image "-"
              mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
              mrmath: [ERROR] error opening image "-"
              mrstats: [ERROR] no filename supplied to standard input (broken pipe?)
              mrstats: [ERROR] error opening image "-"
dwinormalise:

Screenshots / relevant information:

2

Interestingly this was fixed when running in another HCP environment, using the nextflow/21.10.3 module.