Qsiprep Logging error

Software Support
1

Summary of what happened:

I am running qsiprep with version 22.0. However, I got the error shown below and how do I rectify this please?

Command used:

# Execute QSIPrep with Apptainer
apptainer run --containall --writable-tmpfs \
    -B $qsiprepPath:$qsiprepPath \
    -B $outPath:$outPath \
    -B $cachePath:$cachePath \
    -B $licFile:/opt/freesurfer/license.txt \
    qsiprep-0.22.0.sif \
    $qsiprepPath $outPath participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --skip-bids-validation \
    --pepolar-method TOPUP \
    --hmc-transform Affine \
    --b1-biascorrect-stage final \
    --hmc_model eddy \
    --distortion-group-merge none \
    --longitudinal \
    --anatomical-template MNI152NLin2009cAsym \
    --anat-modality T1w \
    --output-resolution 1.2 \
    --participant-label $participant_label \
    --nthreads 5 \
    --low-mem \
    --stop-on-first-crash \
    --verbose \
    --debug all \
    -w $cachePath

error log outputs ):

--- Logging error ---
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1100, in emit
    msg = self.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 943, in format
    return fmt.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 678, in format
    record.message = record.getMessage()
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 368, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/opt/conda/envs/qsiprep/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 133, in main
    qsiprep_wf.run(**config.nipype.get_plugin())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
    result = self._interface.run(cwd=outdir, ignore_exception=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/dsi_studio.py", line 253, in _list_outputs
    config.loggers.interface.info("current dir", os.getcwd())
Message: 'current dir'
Arguments: ('/work/wanglab/eugwueke/datasets/NCANDA_sub95/cache/01_qsiprep/qsiprep_0_22_wf/sub_NCANDA00095_wf/dwi_preproc_ses_Y01_acq_dti60b1000_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi',)
--- Logging error ---
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1100, in emit
    msg = self.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 943, in format
    return fmt.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 678, in format
    record.message = record.getMessage()
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 368, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/opt/conda/envs/qsiprep/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 133, in main
    qsiprep_wf.run(**config.nipype.get_plugin())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
    result = self._interface.run(cwd=outdir, ignore_exception=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/dsi_studio.py", line 255, in _list_outputs
    config.loggers.interface.info("input src", self.inputs.input_src_file)
Message: 'input src'
Arguments: ('/work/wanglab/eugwueke/datasets/NCANDA_sub95/cache/01_qsiprep/qsiprep_0_22_wf/sub_NCANDA00095_wf/dwi_preproc_ses_Y01_acq_dti60b1000_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi/sub-NCANDA00095_ses-Y01_acq-dti60b1000_dwi_LAS_merged.src.gz',)
--- Logging error ---
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1100, in emit
    msg = self.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 943, in format
    return fmt.format(record)
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 678, in format
    record.message = record.getMessage()
  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 368, in getMessage
    msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
  File "/opt/conda/envs/qsiprep/bin/qsiprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 133, in main
    qsiprep_wf.run(**config.nipype.get_plugin())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
    result = self._interface.run(cwd=outdir, ignore_exception=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/dsi_studio.py", line 256, in _list_outputs
    config.loggers.interface.info("split src name", srcname)
Message: 'split src name'
Arguments: ('sub-NCANDA00095_ses-Y01_acq-dti60b1000_dwi_LAS_merged.src.gz',)

How can I rectify this please?

2

Hi @Esther_Samuel and welcome to neurostars!

May you please try the most recent version? As of right now, 1.0.0rc1 on the pennlinc dockerhub channel.

Also this might be that dsistudio sometimes uses emojis which may not be compatible with some clusters. If so, there’s nothing to worry about as long as the rest of the pipeline proceeds to completion.

Best,
Steven

3

Thank you, Steven.

I will do just that.