Unable to open database file

[joey-scanga]

What happened?

Hello,

When running version 25.0.1 in a Docker container, I get an error as soon as Nibabies starts, throwing sqlite3.OperationalError: unable to open database file. What could be happening here?

What command did you use?

#!/bin/bash

subs=($(find /export/scratch1/npad_umn_surfs/work2/bibsnet/ -maxdepth 1 -type d -name "sub-*" -printf "%P\n" | sort | grep -Po '\d+'))
for sub in ${subs[@]}; do
  mkdir -p /export/scratch1/npad_umn_surfs/nibabies_work/${sub}
  docker run --rm -it -u $(id -u):$(id -g) \
    -v /data/sylvester/data1/datasets/npad/umn_surfaces_v2/rawdata:/input \
    -v /data/sylvester/data1/datasets/npad/umn_surfaces_v2/derivatives/nibabies:/output \
    -v /data/sylvester/data1/datasets/npad/umn_surfaces_v2/derivatives/bibsnet:/derivatives \
    -v /export/scratch1/npad_umn_surfs/nibabies_work/${sub}:/work \
    -v ${FREESURFER_LICENSE}:/opt/freesurfer/license.txt \
    nipreps/nibabies:25.0.1 \
    --participant-label $sub \
    -s 01 \
    -d /derivatives \
    --anat-only \
    --cifti-output 91k \
    --project-goodvoxels \
    --random-seed 1234 \
    --fs-license-file /opt/freesurfer/license.txt \
    -w /work \
    --stop-on-first-crash \
    --age-months 1 \
    --surface-recon-method mcribs \
    --norm-csf \
    --multi-step-reg \
    --output-spaces fsLR MNI152NLin6Asym MNI152NLin2009cAsym anat \
    --clean-workdir \
    --skip-bids-validation \
    /input /output participant
done

What version of NiBabies are you using?

25.0.1

Relevant log output

You are using NiBabies-25.0.1, and a newer version of NiBabies is available: 25.0.2.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_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 "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 20, in main
    parse_args()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/parser.py", line 889, in parse_args
    all_subjects = config.execution.layout.get_subjects(scope='raw')
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 199, in __getattr__
    entities = self.get_entities()
               ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 403, in get_entities
    results = query.all()
              ^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2699, in all
    return self._iter().all()  # type: ignore
           ^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2853, in _iter
    result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
                                                  ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2365, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3274, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 148, in __init__
    Connection._handle_dbapi_exception_noconnection(
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 2439, in _handle_dbapi_exception_noconnection
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_dbapi.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: https://sqlalche.me/e/20/e3q8)
^CTraceback (most recent call last):
  File "/opt/conda/envs/nibabies/bin/nibabies", line 5, in <module>
    from nibabies.cli.run import main
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 4, in <module>
    from .. import config
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/config.py", line 94, in <module>
    from templateflow.conf import TF_LAYOUT
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/templateflow/__init__.py", line 42, in <module>
    from templateflow import api
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/templateflow/api.py", line 31, in <module>
    from templateflow.conf import (
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/templateflow/conf/__init__.py", line 194, in <module>
    init_layout()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/templateflow/conf/__init__.py", line 178, in init_layout
    TF_LAYOUT = Layout(
                ^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 177, in __init__
    _indexer(self)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/index.py", line 153, in __call__
    all_bfs, all_tag_dicts = self._index_dir(self._layout._root, self._config)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/index.py", line 260, in _index_dir
    dir_bfs, dir_tag_dicts = self._index_dir(d, config, force=force)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/index.py", line 246, in _index_dir
    bf, tag_dicts = self._index_file(abs_fn, config_entities)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/index.py", line 273, in _index_file
    m = e.match_file(bf)
        ^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/models.py", line 604, in match_file
    m = self.regex.search(f.path)
        ^^^^^^^^^^^^^^^^^^^^^^^^^
KeyboardInterrupt
You are using NiBabies-25.0.1, and a newer version of NiBabies is available: 25.0.2.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_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 "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 20, in main
    parse_args()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/parser.py", line 889, in parse_args
    all_subjects = config.execution.layout.get_subjects(scope='raw')
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 199, in __getattr__
    entities = self.get_entities()
               ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 403, in get_entities
    results = query.all()
              ^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2699, in all
    return self._iter().all()  # type: ignore
           ^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2853, in _iter
    result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
                                                  ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2365, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3274, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 148, in __init__
    Connection._handle_dbapi_exception_noconnection(
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 2439, in _handle_dbapi_exception_noconnection
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_dbapi.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: https://sqlalche.me/e/20/e3q8)
You are using NiBabies-25.0.1, and a newer version of NiBabies is available: 25.0.2.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_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 "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 20, in main
    parse_args()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/parser.py", line 889, in parse_args
    all_subjects = config.execution.layout.get_subjects(scope='raw')
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 199, in __getattr__
    entities = self.get_entities()
               ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/bids/layout/layout.py", line 403, in get_entities
    results = query.all()
              ^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2699, in all
    return self._iter().all()  # type: ignore
           ^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2853, in _iter
    result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
                                                  ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2365, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2241, in _execute_internal
    conn = self._connection_for_bind(bind)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2110, in _connection_for_bind
    return trans._connection_for_bind(engine, execution_options)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 2, in _connection_for_bind
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
                ^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1189, in _connection_for_bind
    conn = bind.connect()
           ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3274, in connect
    return self._connection_cls(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 148, in __init__
    Connection._handle_dbapi_exception_noconnection(
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 2439, in _handle_dbapi_exception_noconnection
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 146, in __init__
    self._dbapi_connection = engine.raw_connection()
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 3298, in raw_connection
    return self.pool.connect()
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 449, in connect
    return _ConnectionFairy._checkout(self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 1263, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 712, in checkout
    rec = pool._do_get()
          ^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/impl.py", line 308, in _do_get
    return self._create_connection()
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 390, in _create_connection
    return _ConnectionRecord(self)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 674, in __init__
    self.__connect()
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 900, in __connect
    with util.safe_reraise():
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/pool/base.py", line 896, in __connect
    self.dbapi_connection = connection = pool._invoke_creator(self)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/create.py", line 646, in connect
    return dialect.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 622, in connect
    return self.loaded_dbapi.connect(*cargs, **cparams)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
(Background on this error at: https://sqlalche.me/e/20/e3q8)
^C

Add any additional information or context about the problem here.

The above log consists of multiple runs, then a keyboard interrupt to stop the script -- they both end on the same sqlite error

[joey-scanga]

UPDATE: This issue went away as soon as I removed the --clean-workdir flag, Nibabies was trying to read from a sqlite database file I'm assuming was removed as a result of this flag

[mgxd]

Good catch - the --clean-workdir flag should really be removed as directory management is more suited to be handled directly by the users.