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nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://www.nipreps.org/dmriprep
Apache License 2.0
65 stars 24 forks source link

[WARNING] Citeproc: citation eddy not found #202

Open celprov opened 1 year ago

celprov commented 1 year ago

What happened?

Everytime I run dMRIPrep this warning appears.

What command did you use?

singularity run -e 
-B $DATADIR/inputs:/data:ro \
-B ${WORKDIR}:/work \
-B ${OUTDIR}:/out \
-B `pwd`/license.txt:/opt/freesurfer/license.txt \
-B `pwd`/filter_file_$SES.json:/filter_file_$SES.json \
-B ${HOME}/.cache/templateflow/tpl-MNI152NLin6Asym/:${HOME}/.cache/templateflow/tpl-MNI152NLin6Asym/ 
$PATCHES \
-B /oak/stanford/groups/russpold/inprocess/cprovins/hcph-pilot/code/dmriprep/dmriprep:/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/ \
/users/cprovins/singularity_images/dmriprep-0.5.0.simg /data /out/dmriprep-0.5.0 participant \
-w /work --bids-filter-file /filter_file_$SES.json --skip-bids-validation \
--nprocs 4 --mem 45G --omp-nthreads 2 --ignore fieldmaps \
--anat-only -vv

What version of the software are you running?

0.5.0

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

--- Logging error ---
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 1034, in emit
    msg = self.format(record)
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 880, in format
    return fmt.format(record)
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 619, in format
    record.message = record.getMessage()
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 380, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/usr/local/miniconda/bin/dmriprep", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/cli/run.py", line 25, in main
    "To opt out, call dmriprep with a `--notrack` flag",
Message: 'Your usage of dmriprep is being recorded using popylar (https://popylar.github.io/). '
Arguments: ('For details, see https://nipreps.github.io/dmriprep/usage.html. ', 'To opt out, call dmriprep with a `--notrack` flag')
--- Logging error ---
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 1034, in emit
    msg = self.format(record)
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 880, in format
    return fmt.format(record)
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 619, in format
    record.message = record.getMessage()
  File "/usr/local/miniconda/lib/python3.7/logging/__init__.py", line 380, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/usr/local/miniconda/bin/dmriprep", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/cli/run.py", line 25, in main
    "To opt out, call dmriprep with a `--notrack` flag",
Message: 'Your usage of dmriprep is being recorded using popylar (https://popylar.github.io/). '
Arguments: ('For details, see https://nipreps.github.io/dmriprep/usage.html. ', 'To opt out, call dmriprep with a `--notrack` flag')
[WARNING] Citeproc: citation eddy not found

Additional information / screenshots

No response