Hi @oesteban & all
no worries, I can always work on my local machine ā¦ but in the long run Iād hope to get all the fancy new tools to work on our cluster ā¦
I just rebuilt the singularity image for the updated fmriprep and reran the code, but again hit the error:
Standard error:
Return code: 137.
180129-02:49:46,557 workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_101_wf.anat_preproc_wf.t1_2_mni" (/mnt/home/schmaelz/work/fmriprep_wf/single_subject_101_wf/anat_preproc_wf/t1_2_mni)
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==1.0.5', 'console_scripts', 'fmriprep')()
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 270, in main
fmriprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, 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 168, in run
self._clean_queue(jobid, graph, result=result))
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, 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 487, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return 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(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 510, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/interfaces/report_base.py", line 54, in _run_interface
ReportCapableInterface, self)._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/interfaces/mni.py", line 147, in _run_interface
term_out = _write_outputs(interface_result.runtime,
AttributeError: 'NoneType' object has no attribute 'runtime'
[schmaelz@dev-intel14 ~]$
I am fairly confident that the dataset would run on your singularity, but have little clue why it doesnāt on mine. As said, it is not too time-critical, but I want to report here also in case others hit similar issues.
best, r