Open jdkent opened 4 years ago
Error when ran again:
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
sys.exit(main())
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 303, in main
fmriprep_wf.write_graph(graph2use="colored", format='svg', simple_form=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 430, in write_graph
outfname = format_dot(dotfilename, format=format)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 1390, in format_dot
formatted_dot, _ = _run_dot(dotfilename, format_ext=format)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py", line 1407, in _run_dot
resource_monitor=False).run()
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/nipype/interfaces/base/core.py", line 1038, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 975, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
dot -Tsvg -o"/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/graph.svg" "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/graph.dot"
Standard output:
Standard error:
Warning: syntax ambiguity - badly delimited number '120065_' in line 2179 of /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/graph.dot splits into two tokens
Error: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/graph.dot: syntax error in line 2179 near '120065'
Return code: 1
delete the graph*
files in the working directory for fmriprep: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/graph*
(follow up, this works to fix this particular error)
Next step was deleting the freesurfer directory entirely for the participant, but this resulted in another error:
200315-11:58:00,540 nipype.workflow WARNING:
Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information:
Node: fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm
Interface: fmriprep.interfaces.freesurfer.PatchedRobustRegister
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 338, in _local_hash_check
cached, updated = self.procs[jobid].is_cached()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 294, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 488, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 515, in _get_inputs
results = loadpkl(results_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 668, in loadpkl
raise e
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 659, in loadpkl
unpkl = pickle.load(pkl_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1440, in __setstate__
self.trait_set( trait_change_notify = trait_change_notify, **state )
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1543, in trait_set
setattr( self, name, value )
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
self.info_text, value))
traits.trait_errors.TraitError: The trait 'T1' of a ReconAllOutputSpec instance is an existing file name, but the path '/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/T1.mgz' does not exist.
200315-11:58:00,593 nipype.workflow WARNING:
Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information:
Node: fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern
Interface: fmriprep.interfaces.freesurfer.FSInjectBrainExtracted
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 338, in _local_hash_check
cached, updated = self.procs[jobid].is_cached()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 294, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 488, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 515, in _get_inputs
results = loadpkl(results_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 668, in loadpkl
raise e
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 659, in loadpkl
unpkl = pickle.load(pkl_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1440, in __setstate__
self.trait_set( trait_change_notify = trait_change_notify, **state )
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1543, in trait_set
setattr( self, name, value )
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
self.info_text, value))
traits.trait_errors.TraitError: The trait 'T1' of a ReconAllOutputSpec instance is an existing file name, but the path '/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/T1.mgz' does not exist.
200315-11:58:02,686 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
200315-11:58:02,793 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm".
200315-11:58:02,796 nipype.workflow ERROR:
Node skull_strip_extern failed to run on host argon-itf-cf49-34.hpc.
200315-11:58:02,829 nipype.workflow ERROR:
Saving crash info to /mnt/Projects/CREST/derivatives/fmriprep/sub-BETTER120044/log/20200315-115448_fb93b1e9-95ad-4522-8453-1fcd9f8aaff3/crash-20200315-115802-ariveradompenciel-skull_strip_extern-c2044b36-c4c2-46c3-9c9f-d7c3f3e924c9.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 408, in run
cached, updated = self.is_cached()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 294, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 488, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 515, in _get_inputs
results = loadpkl(results_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 668, in loadpkl
raise e
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 659, in loadpkl
unpkl = pickle.load(pkl_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1440, in __setstate__
self.trait_set( trait_change_notify = trait_change_notify, **state )
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1543, in trait_set
setattr( self, name, value )
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
self.info_text, value))
traits.trait_errors.TraitError: The trait 'T1' of a ReconAllOutputSpec instance is an existing file name, but the path '/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/T1.mgz' does not exist.
200315-11:58:05,572 nipype.workflow ERROR:
Node fsnative_2_t1_xfm failed to run on host argon-itf-cf49-34.hpc.
200315-11:58:05,573 nipype.workflow ERROR:
Saving crash info to /mnt/Projects/CREST/derivatives/fmriprep/sub-BETTER120044/log/20200315-115448_fb93b1e9-95ad-4522-8453-1fcd9f8aaff3/crash-20200315-115805-ariveradompenciel-fsnative_2_t1_xfm-6adebb56-12c4-4213-a796-3543734cac32.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 408, in run
cached, updated = self.is_cached()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 294, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 488, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 515, in _get_inputs
results = loadpkl(results_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 668, in loadpkl
raise e
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 659, in loadpkl
unpkl = pickle.load(pkl_file)
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1440, in __setstate__
self.trait_set( trait_change_notify = trait_change_notify, **state )
File "/usr/local/miniconda/lib/python3.6/site-packages/traits/has_traits.py", line 1543, in trait_set
setattr( self, name, value )
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
self.info_text, value))
traits.trait_errors.TraitError: The trait 'T1' of a ReconAllOutputSpec instance is an existing file name, but the path '/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/T1.mgz' does not exist.
200315-11:58:30,708 nipype.workflow ERROR:
could not run node: fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern
200315-11:58:30,712 nipype.workflow ERROR:
could not run node: fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm
Need to delete the relevant working directory as well: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf
Script/Job File
Error Message
Potential Solution
delete the working directory and run again:
/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf