Description
Summary
Attempt to submit jobs with SLURMGraph fails
Actual behavior
-bash-4.2$ ./run_fmriprep
180103-15:26:37,49 workflow IMPORTANT:
Running fMRIPREP version 1.0.2:
BIDS dataset path: /homea/inm7/mfalkiew/data/NaKo/BIDS.
Participant list: ['100005'].
Run identifier: 20180103-152636_9b5fa9df-2e8f-4c67-99fb-d3d9f203d1df.
180103-15:26:37,938 workflow IMPORTANT:
Creating bold processing workflow for "/homea/inm7/mfalkiew/data/NaKo/BIDS/sub-100005/func/sub-100005_task-rest_bold.nii.gz" (0.03 GB / 180 TRs).
180103-15:26:38,214 workflow IMPORTANT:
Slice-timing correction will be included.
180103-15:26:38,604 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /homea/inm7/mfalkiew/data/NaKo/BIDS/sub-100005/func/sub-100005_task-rest_bold.nii.gz.
180103-15:26:38,773 workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
Traceback (most recent call last):
File "/homea/inm7/mfalkiew/.linuxbrew/bin/fmriprep", line 11, in
sys.exit(main())
File "/homea/inm7/mfalkiew/.linuxbrew/opt/python3/lib/python3.6/site-packages/fmriprep/cli/run.py", line 270, in main
fmriprep_wf.run(**plugin_settings)
File "/homea/inm7/mfalkiew/.local/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 574, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/homea/inm7/mfalkiew/.local/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 530, in run
graph.predecessors(node)]
File "/homea/inm7/mfalkiew/.local/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 529, in
dependencies[idx] = [nodes.index(prevnode) for prevnode in
AttributeError: 'generator' object has no attribute 'index'
Expected behavior
Pipeline submitted
How to replicate the behavior
Submit jobs with SLURMGraph plugin
Script/Workflow details
Vanilla fmriprep 1.0.2
Platform details:
-bash-4.2$ python3 -c "import nipype; print(nipype.get_info()); print(nipype.version)"
{'pkg_path': '/homea/inm7/mfalkiew/.local/lib/python3.6/site-packages/nipype', 'commit_source': 'installation', 'commit_hash': 'bdb7afc', 'nipype_version': '0.14.0', 'sys_version': '3.6.4 (default, Jan 2 2018, 15:26:07) \n[GCC 5.5.0]', 'sys_executable': '/homea/inm7/mfalkiew/.linuxbrew/opt/python3/bin/python3.6', 'sys_platform': 'linux', 'numpy_version': '1.13.3', 'scipy_version': '1.0.0', 'networkx_version': '2.0', 'nibabel_version': '2.2.1', 'traits_version': '4.6.0'}
0.14.0