Issue with subject IDs in output

Describe the bug When running xcpEngine version 1.2.3, I'm noticing in the output directory that subject IDs are not the same as what is specified in the cohort file (and fMRIPrep output in general).

Cohort file

sub,task,img
sub-01,rest,sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
sub-01,rest,sub-01/func/sub-01_task-rest_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz

Design File Not listing design file contents, as I don't believe this issue is related

Error message

Current processing step:
@1 Localising subject metadata...
·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?·?
·? @1.1 [Parsing subject identifiers]
·? @1.1a [Creating output directory]
·? @1.1b [/N/dcwan/projects/irf/BIDS/BIDS_tutorial/derivatives/xcpEngine-1.2.3/anat/space-MNI152NLin2009cAsym/9001]
·? @1.2 [Initialising space mapping]
·? @1.3 [Initialising derivative maps]
·? @1.4 [Initialising atlas system]
·? @1.5 Ingress
·? @1.5.1 [Native space: 9001_anatomical]
·? @1.5.2a [Standard space: MNI]
·? @1.5.3a [Anatomical space: 9001_anatomical]
source space map '' is not an image
·? @1.5 [Priming analytic audit]
·? @1.6 [Priming quality assessment]

Runtime Information Running using Singularity 3.6.4. Command is:

unset PYTHONPATH; singularity run -B /N/slate/$(whoami):/N/slate/$(whoami) \
        /N/dcwan/projects/irf/containers/xcpEngine-${xcpEngine_version}.simg \
        -d $design_file \
        -c $cohort_file \
        -i $temp_dir \
        -r $fmriprep_data_dir \
        -t 2 \
        -o $final_output_dir

Additional context In the cohort file the subject ID is sub-01; however, in the output, this is changed to 9001. I'm unsure if this has to do with the two runs, but I'm having difficulty understanding why the subject ID is being changed during processing.

PennLINC / xcpEngine

Issue with subject IDs in output #424