fMRIprep 20.2.6 unable to open database file

[QunjunLIANG]

What happened?

I encounter an error when using fMRIprep after updating the version to 20.2.6 by calling ‘fmriprep-docker’. I use fmriprep on my personal computer, and the data is placed on my mobile HD, so I am not sure it is a problem about the permission like issue #2506. Any idea will be appreciated, thanks.

What command did you use?

docker run --rm -it -v /media/lqj/PUS4T/CircleNavigation/NIfTI_BIDS:/data:ro -v
/media/lqj/PUS4T/CircleNavigation/NIfTI_BIDS/derivatives:/out -v
/media/lqj/PUS4T/CircleNavigation/fmriprep_tmp:/work -v
/media/lqj/PUS4T/CircleNavigation/license.txt:/opt/freesurfer/license.txt:ro nipreps/fmriprep:20.2.6
/data /out -w /work participant --participant-label 01 --fs-no-reconall --output-spaces
MNI152NLin6Asym:res-2 --use-aroma --clean-workdir --dummy-scans=0

What version of fMRIPrep are you running?

20.2.6

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py”, line 2336, in _wrap_pool_connect
return fn()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 364, in connect
return _ConnectionFairy._checkout(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 495, in checkout
rec = pool._do_get()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/impl.py”, line 241, in _do_get
return self._create_connection()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 309, in _create_connection
return _ConnectionRecord(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 440, in init
self.__connect(first_connect_check=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 661, in _connect
pool.logger.debug(“Error on connect(): %s”, e)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py”, line 70, in exit
with_traceback=exc_tb,
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py”, line 182, in raise
raise exception
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 656, in __connect
connection = pool._invoke_creator(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py”, line 114, in connect
return dialect.connect(*cargs, **cparams)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py”, line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
sqlite3.OperationalError: unable to open database file

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main
parse_args()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 763, in parse_args
all_subjects = config.execution.layout.get_subjects()
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 174, in getattr
entities = self.get_entities()
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 373, in get_entities
results = query.all()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/query.py”, line 3373, in all
return list(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/query.py”, line 3535, in iter
return self._execute_and_instances(context)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/query.py”, line 3557, in _execute_and_instances
querycontext, self._connection_from_session, close_with_result=True
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/query.py”, line 3572, in _get_bind_args
mapper=self._bind_mapper(), clause=querycontext.statement, **kw
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/query.py”, line 3550, in _connection_from_session
conn = self.session.connection(**kw)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py”, line 1145, in connection
execution_options=execution_options,
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py”, line 1151, in _connection_for_bind
engine, execution_options
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py”, line 433, in _connection_for_bind
conn = bind._contextual_connect()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py”, line 2302, in _contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py”, line 2340, in wrap_pool_connect
e, dialect, self
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py”, line 1584, in handle_dbapi_exception_noconnection
sqlalchemy_exception, with_traceback=exc_info[2], from=e
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py”, line 182, in raise
raise exception
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/base.py”, line 2336, in _wrap_pool_connect
return fn()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 364, in connect
return _ConnectionFairy._checkout(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 495, in checkout
rec = pool._do_get()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/impl.py”, line 241, in _do_get
return self._create_connection()
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 309, in _create_connection
return _ConnectionRecord(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 440, in init
self.__connect(first_connect_check=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 661, in _connect
pool.logger.debug(“Error on connect(): %s”, e)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py”, line 70, in exit
with_traceback=exc_tb,
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py”, line 182, in raise
raise exception
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/pool/base.py”, line 656, in __connect
connection = pool._invoke_creator(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py”, line 114, in connect
return dialect.connect(*cargs, **cparams)
File “/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/engine/default.py”, line 508, in connect
return self.dbapi.connect(*cargs, **cparams)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: http://sqlalche.me/e/13/e3q8)

Additional information / screenshots

No response

[QunjunLIANG]

I am sorry... I should be more careful with the argument "--clean-wkdir". It runs well after comment out the argument.