failed to run on host bogon

Summary

The Head Motion Correction (HMC) did not perform normally.

Actual behavior

Here is a minimal example:

from nipype.workflows.dmri.fsl.artifacts import hmc_pipeline
hmc = hmc_pipeline()
hmc.inputs.inputnode.in_file = 'SE8_NODDI-90_20180318074608_6.nii.gz'
hmc.inputs.inputnode.in_bvec = 'SE8_NODDI-90_20180318074608_6.bvec'
hmc.inputs.inputnode.in_bval = 'SE8_NODDI-90_20180318074608_6_corrected.bval'
hmc.inputs.inputnode.in_mask = 'SE8_NODDI-90_20180318074608_6_brain_mask.nii.gz'
hmc.run()

And the output is as below (sorry it is a bit long):

180320-16:48:35,793 workflow INFO:
     Workflow motion_correct settings: ['check', 'execution', 'logging', 'monitoring']
180320-16:48:35,829 workflow INFO:
     Running serially.
180320-16:48:35,832 workflow INFO:
     [Node] Setting-up "motion_correct.DWICoregistration.MskDilate" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpFqqlSh/motion_correct/DWICoregistration/MskDilate".
180320-16:48:35,849 workflow INFO:
     [Node] Running "MskDilate" ("nipype.interfaces.fsl.maths.MathsCommand"), a CommandLine Interface with command:
fslmaths SE8_NODDI-90_20180318074608_6_brain_mask.nii.gz -nan -kernel sphere 5 -dilM /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/SE8_NODDI-90_20180318074608_6_brain_mask_maths.nii.gz
180320-16:48:35,915 workflow WARNING:
     [Node] Error on "motion_correct.DWICoregistration.MskDilate" (/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpFqqlSh/motion_correct/DWICoregistration/MskDilate)
180320-16:48:35,926 workflow ERROR:
     Node MskDilate failed to run on host bogon.
180320-16:48:35,927 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-164835-pkuclosed-MskDilate-1a35c5ab-f691-4756-8437-fc9cc8549f0f.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1020, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 761, in run_command
    Stream('stdout', proc.stdout),
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/support.py", line 253, in __init__
    self.default_encoding = locale.getdefaultlocale()[1] or 'UTF-8'
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 545, in getdefaultlocale
    return _parse_localename(localename)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 477, in _parse_localename
    raise ValueError, 'unknown locale: %s' % localename
ValueError: unknown locale: UTF-8

180320-16:48:35,938 workflow INFO:
     [Node] Setting-up "motion_correct.SplitDWI" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmp5YTl2K/motion_correct/SplitDWI".
180320-16:48:35,956 workflow INFO:
     [Node] Running "SplitDWI" ("nipype.interfaces.utility.wrappers.Function")
180320-16:48:35,962 workflow WARNING:
     [Node] Error on "motion_correct.SplitDWI" (/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmp5YTl2K/motion_correct/SplitDWI)
180320-16:48:35,971 workflow ERROR:
     Node SplitDWI failed to run on host bogon.
180320-16:48:35,972 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-164835-pkuclosed-SplitDWI-e8cce201-acfb-4d6c-8c31-1ade14537bed.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/utility/wrappers.py", line 144, in _run_interface
    out = function_handle(**args)
  File "<string>", line 12, in hmc_split
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nibabel/loadsave.py", line 40, in load
    raise FileNotFoundError("No such file: '%s'" % filename)
FileNotFoundError: No such file: 'SE8_NODDI-90_20180318074608_6.nii.gz'

180320-16:48:35,979 workflow INFO:
     ***********************************
180320-16:48:35,979 workflow ERROR:
     could not run node: motion_correct.DWICoregistration.MskDilate
180320-16:48:35,979 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-164835-pkuclosed-MskDilate-1a35c5ab-f691-4756-8437-fc9cc8549f0f.pklz
180320-16:48:35,980 workflow ERROR:
     could not run node: motion_correct.SplitDWI
180320-16:48:35,980 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-164835-pkuclosed-SplitDWI-e8cce201-acfb-4d6c-8c31-1ade14537bed.pklz
180320-16:48:35,980 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 602, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run
    report_nodes_not_run(notrun)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/tools.py", line 78, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

It seems that nodes did not perform as they should. For example, “Node MskDilate failed to run on host bogon."

Platform details:

I am using a Mac OS.

The output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)” is: {'nibabel_version': '2.2.1', 'sys_executable': '/Users/pkuclosed/anaconda2/bin/python', 'networkx_version': '2.0', 'numpy_version': '1.13.3', 'sys_platform': 'darwin', 'sys_version': '2.7.14 |Anaconda custom (64-bit)| (default, Oct 5 2017, 02:28:52) \n[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]', 'commit_source': 'installation', 'commit_hash': 'bded0d02', 'pkg_path': '/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype', 'nipype_version': '1.0.1', 'traits_version': '4.6.0', 'scipy_version': '0.19.1'} 1.0.1

Execution environment

In the terminal, I typed python. Then I executed the above code line by line.

Hi @satra

Thank you for the reply. I tried your code with absolute paths, and still got some errors. Would you please make some suggestions?

180320-20:34:13,452 workflow INFO:
     Workflow motion_correct settings: ['check', 'execution', 'logging', 'monitoring']
180320-20:34:13,490 workflow INFO:
     Running serially.
180320-20:34:13,491 workflow INFO:
     [Node] Setting-up "motion_correct.DWICoregistration.MskDilate" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpouwb5t/motion_correct/DWICoregistration/MskDilate".
180320-20:34:13,509 workflow INFO:
     [Node] Running "MskDilate" ("nipype.interfaces.fsl.maths.MathsCommand"), a CommandLine Interface with command:
fslmaths /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/SE8_NODDI-90_20180318074608_6_brain_mask.nii.gz -nan -kernel sphere 5 -dilM /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/SE8_NODDI-90_20180318074608_6_brain_mask_maths.nii.gz
180320-20:34:19,211 workflow WARNING:
     [Node] Error on "motion_correct.DWICoregistration.MskDilate" (/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpouwb5t/motion_correct/DWICoregistration/MskDilate)
180320-20:34:19,223 workflow ERROR:
     Node MskDilate failed to run on host localhost.
180320-20:34:19,225 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203419-pkuclosed-MskDilate-96e505d6-4e96-4ce8-be07-2ec01d591f11.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1020, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 761, in run_command
    Stream('stdout', proc.stdout),
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/support.py", line 253, in __init__
    self.default_encoding = locale.getdefaultlocale()[1] or 'UTF-8'
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 545, in getdefaultlocale
    return _parse_localename(localename)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 477, in _parse_localename
    raise ValueError, 'unknown locale: %s' % localename
ValueError: unknown locale: UTF-8

180320-20:34:19,234 workflow INFO:
     [Node] Setting-up "motion_correct.SplitDWI" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI".
180320-20:34:19,244 workflow INFO:
     [Node] Running "SplitDWI" ("nipype.interfaces.utility.wrappers.Function")
180320-20:34:31,134 workflow INFO:
     [Node] Finished "motion_correct.SplitDWI".
180320-20:34:31,137 workflow INFO:
     [Node] Setting-up "motion_correct.DWICoregistration.SplitDWIs" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpN1u0Vj/motion_correct/DWICoregistration/SplitDWIs".
180320-20:34:31,142 workflow ERROR:
     Node SplitDWIs failed to run on host localhost.
180320-20:34:31,143 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-SplitDWIs-ae272bcc-8828-4194-a296-d3f8ccdeab25.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 424, in run
    cached, updated = self.is_cached()
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 310, in is_cached
    hashed_inputs, hashvalue = self._get_hashval()
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _get_hashval
    self._get_inputs()
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 547, in _get_inputs
    self.set_input(key, deepcopy(output_value))
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 292, in set_input
    setattr(self.inputs, parameter, deepcopy(val))
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
    self.info_text, value))
TraitError: The trait 'in_file' of a SplitInputSpec instance is an existing file name, but the path  '/private/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI/hmc_mov.nii.gz' does not exist.
Error setting node input:
Node: SplitDWIs
input: in_file
results_file: /var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI/result_SplitDWI.pklz
value: /private/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI/hmc_mov.nii.gz

180320-20:34:31,151 workflow INFO:
     [Node] Setting-up "motion_correct.DWICoregistration.InitXforms" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpe0a4u_/motion_correct/DWICoregistration/InitXforms".
180320-20:34:31,167 workflow INFO:
     [Node] Running "InitXforms" ("nipype.interfaces.utility.wrappers.Function")
180320-20:34:31,175 workflow WARNING:
     [Node] Error on "motion_correct.DWICoregistration.InitXforms" (/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpe0a4u_/motion_correct/DWICoregistration/InitXforms)
180320-20:34:31,189 workflow ERROR:
     Node InitXforms failed to run on host localhost.
180320-20:34:31,190 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-InitXforms-ddabec43-7ac9-4ccd-94a5-6e6fe5a0e7a8.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/utility/wrappers.py", line 144, in _run_interface
    out = function_handle(**args)
  File "<string>", line 5, in _checkinitxfm
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/numpy/lib/npyio.py", line 896, in loadtxt
    fh = iter(open(fname, 'U'))
IOError: [Errno 2] No such file or directory: '/private/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI/bval_split.txt'

180320-20:34:31,201 workflow INFO:
     [Node] Setting-up "motion_correct.DWICoregistration.Bias" in "/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpxl74Ui/motion_correct/DWICoregistration/Bias".
180320-20:34:31,220 workflow INFO:
     [Node] Running "Bias" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /private/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpZwPcro/motion_correct/SplitDWI/hmc_ref.nii.gz --mask-image /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/SE8_NODDI-90_20180318074608_6_brain_mask.nii.gz --output hmc_ref_corrected.nii.gz
180320-20:34:31,375 workflow WARNING:
     [Node] Error on "motion_correct.DWICoregistration.Bias" (/var/folders/3w/rk8vrs9j06l1p7xbk30p_hfw0000gn/T/tmpxl74Ui/motion_correct/DWICoregistration/Bias)
180320-20:34:31,386 workflow ERROR:
     Node Bias failed to run on host localhost.
180320-20:34:31,388 workflow ERROR:
     Saving crash info to /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-Bias-587e4058-c888-4a14-8b68-90d2ae77ccc1.pklz
Traceback (most recent call last):
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 498, in run
    version=self.version)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/ants/base.py", line 125, in version
    return Info.version()
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1283, in version
    terminal_output='allatonce').run()
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1020, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 818, in run_command
    result['stdout'] = read_stream(stdout, logger=iflogger)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/utils/filemanip.py", line 674, in read_stream
    default_encoding = encoding or locale.getdefaultlocale()[1] or 'UTF-8'
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 545, in getdefaultlocale
    return _parse_localename(localename)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/locale.py", line 477, in _parse_localename
    raise ValueError, 'unknown locale: %s' % localename
ValueError: unknown locale: UTF-8

180320-20:34:31,396 workflow INFO:
     ***********************************
180320-20:34:31,396 workflow ERROR:
     could not run node: motion_correct.DWICoregistration.MskDilate
180320-20:34:31,396 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203419-pkuclosed-MskDilate-96e505d6-4e96-4ce8-be07-2ec01d591f11.pklz
180320-20:34:31,396 workflow ERROR:
     could not run node: motion_correct.DWICoregistration.SplitDWIs
180320-20:34:31,396 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-SplitDWIs-ae272bcc-8828-4194-a296-d3f8ccdeab25.pklz
180320-20:34:31,396 workflow ERROR:
     could not run node: motion_correct.DWICoregistration.InitXforms
180320-20:34:31,396 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-InitXforms-ddabec43-7ac9-4ccd-94a5-6e6fe5a0e7a8.pklz
180320-20:34:31,397 workflow ERROR:
     could not run node: motion_correct.DWICoregistration.Bias
180320-20:34:31,397 workflow INFO:
     crashfile: /Users/pkuclosed/Desktop/materials/18_spring/PD/converted/SE8/crash-20180320-203431-pkuclosed-Bias-587e4058-c888-4a14-8b68-90d2ae77ccc1.pklz
180320-20:34:31,397 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 602, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run
    report_nodes_not_run(notrun)
  File "/Users/pkuclosed/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/tools.py", line 78, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

nipy / nipype