Hi,
We are running mriqc on HPC and run into this error as follows, any hints will be highly appreciated!
Thank you!
Node segmentation.a213 failed to run on host c23n02.fnam.hpc.internal.
2020-03-10 10:18:21,437 nipype.workflow:ERROR Node segmentation.a213 failed to run on host c23n02.fnam.hpc.internal.
200310-10:18:21,451 nipype.workflow ERROR:
Saving crash info to /gpfs/ysm/scratch60/la/xs266/la/pid_fmri_qc/logs/crash-20200310-101821-xs266-segmentation.a213-4fab56cb-88ff-4006-b66e-74af1c3b3ddc.txt
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 472, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 563, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 643, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 375, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 758, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 695, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
fast -t 1 -o segment -g -S 1 /gpfs/ysm/scratch60/la/xs266/la/work/workflow_enumerator/anatMRIQCT1w/in_file…gpfs…ysm…scratch60…landi…xs266…la…pid_BIDS…sub-9088…ses-1…an$
Standard output: