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CREST sub-ACT05: Node validate failed to run on host argon-lc-i18-19.hpc #20

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ariveradompenciel opened this issue Jul 14, 2020 · 1 comment
Open

CREST sub-ACT05: Node validate failed to run on host argon-lc-i18-19.hpc #20

ariveradompenciel opened this issue Jul 14, 2020 · 1 comment
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argon fmriprep issue when running fmriprep singularity

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@ariveradompenciel
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Script/Job File

#!/bin/bash

#$ -pe smp 16
#$ -q UI
#$ -m bea
#$ -M [email protected]
#$ -o /Shared/vosslabhpc/Projects/CREST/code/fmriprep/out/
#$ -e /Shared/vosslabhpc/Projects/CREST/code/fmriprep/err/
OMP_NUM_THREADS=10
singularity run -H ${HOME}/singularity_home -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg \
/mnt/Projects/CREST/ /mnt/Projects/CREST/derivatives \
participant --participant_label ACT05 \
-w /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep \
--write-graph --mem_mb 35000 --omp-nthreads 10 --nthreads 16 --use-aroma \
--output-space template \
--template MNI152NLin2009cAsym \
--fs-license-file /mnt/UniversalSoftware/freesurfer_license.txt

Email Message

Job 3458324 (sub-ACT05.job) Complete
User             = ariveradompenciel
Queue            = [email protected]
Host             = argon-lc-i18-19.hpc
Start Time       = 07/08/2020 08:51:48
End Time         = 07/08/2020 17:36:38
User Time        = 00:31:33
System Time      = 00:00:10
Wallclock Time   = 08:44:50
CPU              = 22:45:38
Max vmem         = 6.526G
Exit Status      = 1

Output File

200708-08:52:43,552 nipype.interface WARNING:
	 No 't2w' images found for sub-<undefined>
200708-08:52:43,552 nipype.interface WARNING:
	 No 'flair' images found for sub-<undefined>
200708-08:52:43,552 nipype.interface WARNING:
	 No 'fmap' images found for sub-<undefined>
200708-08:52:43,552 nipype.interface WARNING:
	 No 'sbref' images found for sub-<undefined>
200708-08:52:43,552 nipype.interface WARNING:
	 No 'roi' images found for sub-<undefined>
200708-08:52:43,562 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_ACT05_wf.bidssrc".
200708-08:52:43,636 nipype.workflow INFO:
	 [Node] Setting-up "fmriprep_wf.single_subject_ACT05_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_ACT05_wf/func_preproc_task_rest_wf/bold_reference_wf/validate".
200708-08:52:43,646 nipype.workflow INFO:
	 [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200708-08:52:43,776 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_wf.single_subject_ACT05_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" (/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_ACT05_wf/func_preproc_task_rest_wf/bold_reference_wf/validate)
200708-08:52:45,252 nipype.workflow ERROR:
	 Node validate failed to run on host argon-lc-i18-19.hpc.
200708-08:52:45,264 nipype.workflow ERROR:
	 Saving crash info to /mnt/Projects/CREST/derivatives/fmriprep/sub-ACT05/log/20200708-085159_864e057c-c4b7-4681-b93b-f5e3c1c812e8/crash-20200708-085245-ariveradompenciel-validate-b0ead8bb-636f-4875-8a14-f3d4468c5374.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/images.py", line 422, in _run_interface
    img.to_filename(out_fname)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/filebasedimages.py", line 334, in to_filename
    self.to_file_map()
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/analyze.py", line 1053, in to_file_map
    data = self.get_data()
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
    data = np.asanyarray(self._dataobj)
  File "/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/numeric.py", line 544, in asanyarray
    return array(a, dtype, copy=False, order=order, subok=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 356, in __array__
    raw_data = self.get_unscaled()
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 351, in get_unscaled
    mmap=self._mmap)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/volumeutils.py", line 525, in array_from_file
    infile.seek(offset)
  File "indexed_gzip/indexed_gzip.pyx", line 430, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1

Error (stderr file)

/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'CITATION'
/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:116: UserWarning: 'dataset_description.json' file is missing from project root. You may want to set the root path to a valid BIDS project.
  warnings.warn("'dataset_description.json' file is missing from "
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.6/site-packages/nilearn/image/resampling.py:518: UserWarning: Casting data from int32 to float32
  warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
Errors occurred while generating reports for participants: ACT05 (1).
@ariveradompenciel ariveradompenciel added fmriprep issue when running fmriprep singularity argon labels Jul 14, 2020
@jdkent
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jdkent commented Jul 14, 2020

Looks like you've ran into an fmriprep bug sadly.
The easiest solution is to upgrade the fmriprep singularity image to 1.2.4 where the pull request to fix the bug was merged into the code. Since 1.2.4 is still a bugfix release, the processing of the images should remain the same.

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@jdkent @ariveradompenciel