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singularity run fmriprep-1.3.0.simg /home/gholland/data/bias_task/fmriprep_sourcedata/ /home/gholland/data/bias_task/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [WARN] You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8 - EFFECTIVE_ECHO_SPACING_NOT_DEFINED)
./sub-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-03_bold.nii
2: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)
./sub-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-03_bold.nii
3: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)
./sub-01/anat/sub-01_T1w.nii
Summary: Available Tasks: Available Modalities:
100 Files, 41.27GB Random dot motion task with value-based biases T1w
14 - Subjects bold
1 - Session fieldmap
If you have any questions please post on https://neurostars.org/tags/bids
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:71: DeprecationWarning: dist() and linux_distribution() functions are deprecated in Python 3.5
= platform.linux_distribution()[:2]
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:847: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
is_decorating = not kwargs and len(args) == 1 and isinstance(args[0], collections.Callable)
/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/param.py:30: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
_KNOWN_ARGS = getargspec(argparse.Action.__init__)[0] + ['action']
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:216: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
args, varargs, varkw, defaults = getargspec(func)
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190208-14:54:52,797 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.3.0:
* BIDS dataset path: /home/gholland/data/bias_task/fmriprep_sourcedata.
* Participant list: ['01'].
* Run identifier: 20190208-145452_dffae0c2-129b-45e5-8719-daff90cb9157.
/usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping, Set, Iterable
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:480: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
argspec = getargspec(call)
[WARNING] It is highly recommended to configure git first (set both user.name and user.email) before using DataLad. Failed to verify that git is configured: CommandError: command '['git', 'config', 'user.name']' failed with exitcode 1
| Failed to run ['git', 'config', 'user.name'] under None. Exit code=1. out= err= [cmd.py:run:530]CommandError: command '['git', 'config', 'user.email']' failed with exitcode 1
| Failed to run ['git', 'config', 'user.email'] under None. Exit code=1. out= err= [cmd.py:run:530]. Some operations might fail or not perform correctly.
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:480: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
argspec = getargspec(call)
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 751, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 218, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 461, in init_single_subject_wf
name="anat_preproc_wf",
File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 237, in init_anat_preproc_wf
omp_nthreads=omp_nthreads)
File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 621, in init_skullstrip_ants_wf
t1_skull_strip.inputs.brain_template = get_template(skull_strip_template, 'res-01_T1w.nii.gz')
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 24, in get
out_file = api.get(filepath)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 478, in eval_func
return return_func(generator_func)(*args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 466, in return_func
results = list(results)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 421, in generator_func
result_renderer, result_xfm, _result_filter, **_kwargs):
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 490, in _process_results
for res in results:
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/distribution/get.py", line 622, in __call__
jobs=jobs):
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/gitrepo.py", line 301, in newfunc
result = func(self, files_new, *args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1300, in get
files, ['--not', '--in', 'here'])
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1361, in _get_expected_files
'find', opts=expr, files=files
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 2381, in _run_annex_command_json
raise e
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 2297, in _run_annex_command_json
**kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1053, in _run_annex_command
raise e
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1045, in _run_annex_command
return self.cmd_call_wrapper.run(cmd_list, env=env, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 670, in run
cmd, env=self.get_git_environ_adjusted(env), *args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 530, in run
raise CommandError(str(cmd), msg, status, out[0], out[1])
datalad.support.exceptions.CommandError: CommandError: command '['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz']' failed with exitcode 1
Failed to run ['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz'] under '/opt/templateflow/tpl-OASIS30ANTs'. Exit code=1. out= err=git-annex: .git/annex/journal.lck: openFd: permission denied (Permission denied)
>gholland@r11n13:~$ singularity build ./fmriprep-1.3.0.post1.simg docker://poldracklab/fmriprep:1.3.0.post1
Docker image path: index.docker.io/poldracklab/fmriprep:1.3.0.post1
Cache folder set to /home/gholland/.singularity/docker
[11/11] |===================================| 100.0%
Importing: base Singularity environment
Exploding layer: sha256:c832082614738021cf51d68e84457a45a3f85dbe0ddbb93000c5dc5aae77fe93.tar.gz
Exploding layer: sha256:6e1a85c1d66a18674bdb5cee0a7d6b294aa4f1921d3a13074004d00485868051.tar.gz
Exploding layer: sha256:f1320ef45e201689247f36b8e037ed8de21532f952be224586cb96b43a495f36.tar.gz
Exploding layer: sha256:5a6ab6e6fbf62623bce0db5c75f3775f287c7b86cd0152b01ab09275f1d9f540.tar.gz
Exploding layer: sha256:6fd240c277673683f0b16a0d7903c036c307954976e19e2f82a6873327d1d69b.tar.gz
Exploding layer: sha256:4b9b9707336e4f14ace065404fd20bd27ef049f3090e74e9fe1db049bb4883f3.tar.gz
Exploding layer: sha256:862caf442a1c3ae107b5b7539899c42945233bc57ff2e5987a85ecf610691a39.tar.gz
Exploding layer: sha256:f86ffe633d29b22adf7c810c166695816f0d69013a6d7939b70151246421c865.tar.gz
Exploding layer: sha256:953c27ee92677735d70fcd23a8701e17fe9e45b601e99bbecd61612568806d56.tar.gz
Exploding layer: sha256:59d261ca002b69555013acafd4c3880a1a603f7a2f0876847ce6ec91cb99e0bc.tar.gz
Exploding layer: sha256:d6313008e492027c0ee047bf8f7b2bd84707649cec054ddf8d1678f818a778ae.tar.gz
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
Exploding layer: sha256:b7a8f03d9b42a0a26b4d165f808de8938282760b3d82f46528032cc4aae50410.tar.gz
Exploding layer: sha256:7b4148533d5e1c73822ffbda35cc6ac8e9782b8854e50590268b7ec5d881c5e7.tar.gz
Exploding layer: sha256:66108217b41f85144eacfccd54c79205289306196b685455067d07e1988264b1.tar.gz
Exploding layer: sha256:32a8952ad0b54263cfa9100cdc776f8bbf68e0162240494e0e0dc267e25d4852.tar.gz
Exploding layer: sha256:6fa7b3c219ef9f59ab93946dcf3b3ace36135b1337270e28ebf87d3617e82b04.tar.gz
Exploding layer: sha256:7e85f3579a06c5f0384cf0406af3f22a6ba4701ee3c0ddc588ec8b94f04fd834.tar.gz
Exploding layer: sha256:7a0f6d325044b059b85f161aff11b3960d3abb2a1b7905a338dc0701ae156d67.tar.gz
Exploding layer: sha256:faf4f6f709593572999bd40b7de1078b1c3bec2572c9f7f8a3112ed2b4b9885c.tar.gz
Exploding layer: sha256:8154532e2fbf225db38bef9435a0e629cf09ecff7497a25b2f7a4da05ba216f9.tar.gz
Exploding layer: sha256:97e6d1977928848f4ccc0e361065ec672b320e8a007a3dfa23833d9974d649ac.tar.gz
Exploding layer: sha256:ef44147ae9f44187b724f03ab5aa23f63bcb988d0a8c9c828011aa8f591c5f53.tar.gz
Exploding layer: sha256:908dfea094f5583de50ac5857a8cab0bde04c8b2072682796f81d41f7ab569c4.tar.gz
Exploding layer: sha256:3850088e9de30180d91500fafb721ecc1fae7f77e2681481a36c464467d6ffc8.tar.gz
Exploding layer: sha256:8d643d58a9ca391e105ae405636392cc4482b71dffa83ae197617f13371b3232.tar.gz
Exploding layer: sha256:92372612f2613566cc079c178d483dca796fdd9b8989a02247a0ee49370b7018.tar.gz
Exploding layer: sha256:e54d42c2794749949f0c4548af71bc50b96f3aa592daef3a2502257146dd48a4.tar.gz
Exploding layer: sha256:6a72ec30285c2547fbf3668891383756fb0f3d776b5e61ce34966ff3bcdd59e4.tar.gz
Exploding layer: sha256:80ec24e086ec6a957437484a3894dab4428d6a59846c72b1d5b3b6a15141f771.tar.gz
Exploding layer: sha256:fc4d760f6fab88ee750f9a601ef4b0c61e4b09246ef23915d256571e481bb933.tar.gz
Exploding layer: sha256:584a31f338b0089cc104276cbb21ccaa1fc8542c02447bdf2b8e43b544174118.tar.gz
Exploding layer: sha256:bbe7bf41ba1968971b4459d21613f21cf379373951f2906c92f64f72e623fff2.tar.gz
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
Building Singularity image...
Singularity container built: ./fmriprep-1.3.0.post1.simg
Cleaning up...
gholland@r11n13:~$ singularity run fmriprep-1.3.0.post1.simg /home/gholland/data/bias_task/fmriprep_sourcedata/ /home/gholland/data/bias_task/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [WARN] You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8 - EFFECTIVE_ECHO_SPACING_NOT_DEFINED)
./sub-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-03_bold.nii
2: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)
./sub-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
./sub-01/func/sub-01_task-randomdotmotion_run-03_bold.nii
3: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)
./sub-01/anat/sub-01_T1w.nii
Summary: Available Tasks: Available Modalities:
100 Files, 41.27GB Random dot motion task with value-based biases T1w
14 - Subjects bold
1 - Session fieldmap
If you have any questions please post on https://neurostars.org/tags/bids
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:71: DeprecationWarning: dist() and linux_distribution() functions are deprecated in Python 3.5
= platform.linux_distribution()[:2]
/usr/local/miniconda/lib/python3.7/site-packages/datalad/utils.py:847: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
is_decorating = not kwargs and len(args) == 1 and isinstance(args[0], collections.Callable)
/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/param.py:30: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
_KNOWN_ARGS = getargspec(argparse.Action.__init__)[0] + ['action']
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:216: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
args, varargs, varkw, defaults = getargspec(func)
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190209-08:41:26,369 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.3.0.post1:
* BIDS dataset path: /home/gholland/data/bias_task/fmriprep_sourcedata.
* Participant list: ['01'].
* Run identifier: 20190209-084126_5be6c13e-35e3-40de-9a91-7158f8b77373.
/usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping, Set, Iterable
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:480: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
argspec = getargspec(call)
[WARNING] It is highly recommended to configure git first (set both user.name and user.email) before using DataLad. Failed to verify that git is configured: CommandError: command '['git', 'config', 'user.name']' failed with exitcode 1
| Failed to run ['git', 'config', 'user.name'] under None. Exit code=1. out= err= [cmd.py:run:530]CommandError: command '['git', 'config', 'user.email']' failed with exitcode 1
| Failed to run ['git', 'config', 'user.email'] under None. Exit code=1. out= err= [cmd.py:run:530]. Some operations might fail or not perform correctly.
/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/base.py:480: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
argspec = getargspec(call)
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 751, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 218, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 461, in init_single_subject_wf
name="anat_preproc_wf",
File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 237, in init_anat_preproc_wf
omp_nthreads=omp_nthreads)
File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 621, in init_skullstrip_ants_wf
t1_skull_strip.inputs.brain_template = get_template(skull_strip_template, 'res-01_T1w.nii.gz')
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 24, in get
out_file = api.get(filepath)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 478, in eval_func
return return_func(generator_func)(*args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 466, in return_func
results = list(results)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 421, in generator_func
result_renderer, result_xfm, _result_filter, **_kwargs):
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/interface/utils.py", line 490, in _process_results
for res in results:
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/distribution/get.py", line 622, in __call__
jobs=jobs):
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/gitrepo.py", line 301, in newfunc
result = func(self, files_new, *args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1300, in get
files, ['--not', '--in', 'here'])
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1361, in _get_expected_files
'find', opts=expr, files=files
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 2381, in _run_annex_command_json
raise e
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 2297, in _run_annex_command_json
**kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1053, in _run_annex_command
raise e
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/support/annexrepo.py", line 1045, in _run_annex_command
return self.cmd_call_wrapper.run(cmd_list, env=env, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 670, in run
cmd, env=self.get_git_environ_adjusted(env), *args, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/datalad/cmd.py", line 530, in run
raise CommandError(str(cmd), msg, status, out[0], out[1])
datalad.support.exceptions.CommandError: CommandError: command '['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz']' failed with exitcode 1
Failed to run ['git', '-c', 'receive.autogc=0', '-c', 'gc.auto=0', 'annex', 'find', '--json', '--not', '--in', 'here', '--', 'tpl-OASIS30ANTs_res-01_T1w.nii.gz'] under '/opt/templateflow/tpl-OASIS30ANTs'. Exit code=1. out= err=git-annex: .git/annex/journal.lck: openFd: permission denied (Permission denied)
@sulantha2006

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sulantha2006 commented Feb 12, 2019

Any idea why this occurs? I have the same issue.

@neuro-kf

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neuro-kf commented Feb 13, 2019

Same issue but with version 1.3.0.post1 on singularity

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