Dear there,
I got this error when I run CloudMap EMS Variant Density Mapping workflow for
Depth of Coverage on the local Galaxy instance on Mac. In fact, it works fine
for Depth of Coverage when I run another workflow (Unmapped Mutant workflow)
locally.
I really appreciate you guys for helping me to figure out so many problems!
Thanks a lot!
Best,
Xiaofei
Traceback (most recent call last):
File
"/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 152, in prepare_job
job_wrapper.prepare()
File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 652, in prepare
if job.user is None and job.galaxy_session is None:
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py",
line 168, in __get__
return self.impl.get(instance_state(instance),dict_)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py",
line 453, in get
value = self.callable_(state, passive)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py",
line 508, in _load_for_state
return self._emit_lazyload(session, state, ident_key)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py",
line 552, in _emit_lazyload
return q._load_on_ident(ident_key)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
line 2512, in _load_on_ident
return q.one()
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
line 2184, in one
ret = list(self)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
line 2227, in __iter__
return self._execute_and_instances(context)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
line 2242, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) database is locked u'SELECT galaxy_user.id
AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time,
galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS
galaxy_user_email, galaxy_user.username AS galaxy_user_username,
galaxy_user.password AS galaxy_user_password, galaxy_user.external AS
galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id,
galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS
galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage,
galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS
galaxy_user_activation_token \nFROM galaxy_user \nWHERE galaxy_user.id = ?' (1,)
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