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Could not generate CITATION.html file #3157

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celprov opened this issue Nov 22, 2023 · 0 comments
Open

Could not generate CITATION.html file #3157

celprov opened this issue Nov 22, 2023 · 0 comments
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@celprov
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celprov commented Nov 22, 2023

What happened?

The workflow still runs successfully until the end, but this error is reported.

What command did you use?

DATADIR="/oak/stanford/groups/russpold/inprocess/cprovins/hcph-dataset/"
DERIVATIVEDIR="/oak/stanford/groups/russpold/inprocess/cprovins/hcph-derivatives"
CODEDIR="/oak/stanford/groups/russpold/inprocess/cprovins/code"
SUB="sub-001"
STUDY=`basename $DATADIR`
IMG="/oak/stanford/groups/russpold/users/cprovins/singularity_images/fmriprep-23.2.0a2.simg"
WORKDIR="${L_SCRATCH}/fmriprep-23.2.0a2/${STUDY}/"
OUTDIR="${DERIVATIVEDIR}"


singularity run -e -B $DATADIR:/data:ro \
-B ${WORKDIR}:/work \
-B ${OUTDIR}:/out \
-B $CODEDIR/license.txt:/opt/freesurfer/license.txt \
-B $CODEDIR/filter_file_undistorted.json:/filter_file_undistorted.json \
/data /out/fmriprep-23.2.0a2 participant \
-w /work --bids-filter-file /filter_file_undistorted.json --anat-only --skip_bids_validation \
--nprocs 4 --mem 45G --omp-nthreads 16 \
-vv

What version of fMRIPrep are you running?

23.2.0a2

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Could not generate CITATION.html file:
pandoc -s --bibliography /out/fmriprep-23.2.0a2/logs/CITATION.bib --citeproc --metadata pagetitle="fMRIPrep citation boilerplate" /out/fmriprep-23.2.0a2/logs/CITATION.md -o /out/fmriprep-23.2.0a2/logs/CITATION.html

Additional information / screenshots

No response

@celprov celprov added the bug label Nov 22, 2023
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