'Workflow did not execute cleanly' Error [MRIQC]

[sadevp]

Hello,

Please see the error logs when running MRIQC on this dataset: https://openneuro.org/datasets/ds001105/versions/00001

I am receive an error saying that 'workflow did not execute cleanly', followed by Error Response from Daemon: No Such Container. This may be related to this issue: OpenNeuroOrg/openneuro#131

Here is what the error says:

Traceback (most recent call last):
File "/usr/local/miniconda/bin/mriqc", line 11, in
load_entry_point('mriqc==0.9.8.post1', 'console_scripts', 'mriqc')()
File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py", line 325, in main
workflow.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 590, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 279, in run
report_nodes_not_run(notrun)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 101, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details
Error response from daemon: No such container: 375151cb-721a-4abb-a6fe-ca187b71ead1-lock
No lock found for 375151cb-721a-4abb-a6fe-ca187b71ead1

[chrisgorgo]

To dive deeper into MRIQC issues you can look into the logs sub directory

From that crash file you will learn that the specific error is:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 52, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 372, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 613, in _run_command
    result = self._interface.run()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1083, in run
    runtime = self._run_wrapper(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1757, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/common/report.py", line 53, in _run_interface
    ReportCapableInterface, self)._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1791, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1715, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
melodic -i /usr/local/src/mriqc/work/workflow_enumerator/funcMRIQC/_in_file_..snapshot..data..sub-013..func..sub-013_task-mentalstates_run-3_bold.nii.gz/reorient_and_discard/sub-013_task-mentalstates_run-3_bold.nii.gz --nobet --nomask --no_mm -o /usr/local/src/mriqc/work/workflow_enumerator/funcMRIQC/_in_file_..snapshot..data..sub-013..func..sub-013_task-mentalstates_run-3_bold.nii.gz/ICA
Standard output:

Standard error:
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

bad_alloc means that the app was not able to allocate enough memory. This unfortuantelly happens with MRIQC when the ICA option is turned on and we don't have a good way to avoid it. Try running it without ICA option.

[sadevp]

I received this error again after running this dataset: https://openneuro.org/datasets/ds000011/versions/00001?app=MRIQC&version=46&job=f5e0feed-96f7-41fc-ab29-5fc6f1225431

I did not have the ICA option turned on. You can see that the error only appears for one of the participants.

[chrisgorgo]

@sadevp

This seems to me like a completely different error:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 407, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 517, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1086, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
    out = function_handle(**args)
  File "<string>", line 10, in reorient_and_discard_non_steady
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/funcs.py", line 225, in as_closest_canonical
    arr = img.get_data()
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/spatialimages.py", line 572, in get_data
    data = np.asanyarray(self._dataobj)
  File "/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/numeric.py", line 583, 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 145, in __array__
    raw_data = self.get_unscaled()
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 140, in get_unscaled
    mmap=self._mmap)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/volumeutils.py", line 524, in array_from_file
    n_read = infile.readinto(data_bytes)
  File "/usr/local/miniconda/lib/python3.6/gzip.py", line 276, in read
    return self._buffer.read(size)
  File "/usr/local/miniconda/lib/python3.6/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/usr/local/miniconda/lib/python3.6/gzip.py", line 471, in read
    uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid block type

[sadevp]

I was citing the error at the end of the error log. Should I create a new issue for the error you've identified above?

[chrisgorgo]

The error at the end of the log indicates that something went wrong, but unfortunately many things can go wrong. With MRIQC it's easiest to look at the crashfiles in results. In this case the error indicates that this file sub-09/func/sub-09_task-Classificationprobewithoutfeedback_bold.nii.gz is corrupted. Could you dig a bit more into this and figure out if the version on OpenNeuro is corrupted (just open it and read it in nibabel - get_data()) or the source data that you uploaded is corrupted?

[sadevp]

The original file on openfmri appears to be corrupted, after trying to run in nibabel, I get this error:

Traceback (most recent call last):
File "", line 1, in
File "/Applications/anaconda/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
data = np.asanyarray(self._dataobj)
File "/Applications/anaconda/lib/python3.6/site-packages/numpy/core/numeric.py", line 583, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File "/Applications/anaconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 290, in array
raw_data = self.get_unscaled()
File "/Applications/anaconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 285, in get_unscaled
mmap=self._mmap)
File "/Applications/anaconda/lib/python3.6/site-packages/nibabel/volumeutils.py", line 524, in array_from_file
n_read = infile.readinto(data_bytes)
File "/Applications/anaconda/lib/python3.6/gzip.py", line 276, in read
return self._buffer.read(size)
File "/Applications/anaconda/lib/python3.6/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/Applications/anaconda/lib/python3.6/gzip.py", line 471, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid block type

img.get_data()

[oesteban]

I reported this feature request to the bids-validator repo: https://github.com/INCF/bids-validator/issues/297

But yes, that file should be revised in openfmri (and fix it if possible).

[chrisgorgo]

@sadevp please bring this up with @suyashdb so it will not get lost