Hi preppers!
I’ve been trying to run a command similar to below on fmriprep1.5.0.rc1 on our HPC cluster and seem to be having some problems:
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An OSError in my main logfile indicating that it can’t find elementary data that I’m assuming should just be copied into the derivates folder. The script continues well after this though but eventually hangs.
-
A permissions error that results in several crashes. I’ve seen a few errors like this reported on the site, but they seem to have only been noted when running under singularity (and now apparently fixed).
I can’t attach the logs as a new user but have pasted in relevant excerpts below. Any guidance would be super appreciated 
Cheers,
Arjun
A) Command:
fmriprep /data/project/abc/03_Sorted/02C_Faces_BIDS /data/project/abc/03_Sorted/02D_fmriprep_Faces participant -w derivatives --participant_label $i -t faces --longitudinal --output-spaces MNIPediatricAsym:cohort-3 --use-aroma --dummy-scans 0 --ignore fieldmaps --fs-license-file /data/project/abc/X_Scripts_AS/license.txt
B) Crash example (there are two others but all seem to reference the same issue):
Node: fmriprep_wf.single_subject_ABC004_wf.anat_preproc_wf.anat_norm_wf.msk_select
Working directory: /data/project/abc/03_Sorted/02C_Faces_BIDS/derivatives/fmriprep_wf/single_subject_ABC004_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/msk_select
Node inputs:
desc = brain
function_str = def _get_template(template, template_spec, suffix='T1w', desc=None):
from niworkflows.utils.misc import get_template_specs
template_spec['suffix'] = suffix
template_spec['desc'] = desc
return get_template_specs(template, template_spec=template_spec)[0]
suffix = mask
template = MNIPediatricAsym
template_spec = {'cohort': '3', 'suffix': 'mask', 'desc': 'brain', 'atlas': None, 'resolution': 1}
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 316, in _send_procs_to_workers
self.procs[jobid].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/utility/wrappers.py", line 144, in _run_interface
out = function_handle(**args)
File "<string>", line 5, in _get_template
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/utils/misc.py", line 50, in get_template_specs
tpl_target_path = get_template(in_template, **template_spec)
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 39, in get
_s3_get(filepath)
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 139, in _s3_get
with filepath.open('wb') as f:
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1176, in open
opener=self._opener)
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1030, in _opener
return self._accessor.open(self, flags, mode)
OSError: [Errno 30] Read-only file system: '/home/fmriprep/.cache/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_desc-brain_mask.nii.gz'
C) File not found example. There is alot more but thought this gives the idea:
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 487, in run
self, report_type='postexec', is_mapnode=isinstance(self, MapNode))
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 149, in write_report
result = node.result # Locally cache result
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 197, in result
return _load_resultfile(self.output_dir(), self.name)[0]
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 359, in load_resultfile
basedir=path).items()):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 478, in modify_paths
val, relative=relative, basedir=basedir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 484, in modify_paths
modify_paths(val, relative=relative, basedir=basedir))
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 498, in modify_paths
raise IOError('File %s not found' % out)
OSError: File /data/project/abc/03_Sorted/02C_Faces_BIDS/derivatives/fmriprep_wf/single_subject_ABC004_wf/func_preproc_ses_B_task_faces_wf/func_derivatives_wf/raw_sources/sub-ABC004/ses-B/func/sub-ABC004_ses-B_task-faces_bold.nii.gz not found