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,)