Summary of what happened:
Command used (and if a helper script was used, a link to the helper script or the command generated):
I ran the following code:
sudo docker run --rm \
-ti \
-v /media/share/Member/eden/retinotopy:/data:ro \
-v /media/share/Member/eden/retinotopy/step1:/out \
-v /media/share/Member/eden/retinotopy/work:/work \
-v /home/eden/license.txt:/opt/freesurfer/license.txt \
--shm-size="10g" \
nipreps/fmriprep:latest \
/data /out participant \
--fs-license-file /opt/freesurfer/license.txt \
--use-aroma \
--notrack \
--output-spaces T1w MNI152NLin2009cAsym:res-2 \
--fs-no-reconall \
--use-syn-sdc \
--nthreads 16 \
--mem_mb 32000 \
--work-dir /work \
--skip_bids_validation
Version:
Environment (Docker, Singularity, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
However, I encountered the following issue:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1276, in _execute_context
self.dialect.do_execute(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 608, in do_execute
cursor.execute(statement, parameters)
sqlite3.OperationalError: database is locked
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/fmriprep", line 8, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/run.py", line 43, in main
parse_args()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/parser.py", line 775, in parse_args
config.from_dict({})
File "/opt/conda/lib/python3.9/site-packages/fmriprep/config.py", line 675, in from_dict
execution.load(settings, init=initialize('execution'), ignore=ignore)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/config.py", line 232, in load
cls.init()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/config.py", line 476, in init
cls._layout = BIDSLayout(
File "/opt/conda/lib/python3.9/site-packages/bids/layout/layout.py", line 149, in __init__
self.connection_manager = ConnectionManager(
File "/opt/conda/lib/python3.9/site-packages/bids/layout/db.py", line 45, in __init__
self.reset_database(init_args, config)
File "/opt/conda/lib/python3.9/site-packages/bids/layout/db.py", line 104, in reset_database
Base.metadata.create_all(self.engine)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/schema.py", line 4664, in create_all
bind._run_visitor(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 2095, in _run_visitor
conn._run_visitor(visitorcallable, element, **kwargs)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1656, in _run_visitor
visitorcallable(self.dialect, self, **kwargs).traverse_single(element)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single
return meth(obj, **kw)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/ddl.py", line 783, in visit_metadata
self.traverse_single(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/visitors.py", line 145, in traverse_single
return meth(obj, **kw)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/ddl.py", line 827, in visit_table
self.connection.execute(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1011, in execute
return meth(self, multiparams, params)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection
return connection._execute_ddl(self, multiparams, params)
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1068, in _execute_ddl
ret = self._execute_context(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1316, in _execute_context
self._handle_dbapi_exception(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1510, in _handle_dbapi_exception
util.raise_(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 1276, in _execute_context
self.dialect.do_execute(
File "/opt/conda/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 608, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked
[SQL:
CREATE TABLE layout_info (
root VARCHAR NOT NULL,
absolute_paths BOOLEAN,
_derivatives VARCHAR,
_config VARCHAR,
PRIMARY KEY (root),
CHECK (absolute_paths IN (0, 1))
)
]
(Background on this error at: http://sqlalche.me/e/13/e3q8)
Screenshots / relevant information:
In the past several times, this code was working!
Btw, I used control+c to stop the preprocessing many times.
Then tried again, and it showed this error.
I had tried “sudo rm the dataset and bulid a new one again”
or gave the permission “chmod 777”
But it still happened.