Hi Todd, just to be sure, you are running know postgresql as Galaxy database, or? These locking error is only known from sqlite as far as I know. Can you double check to database backend. Thanks, Bjoern

Hi All, We have been having issues with workflows generating intermittent errors using sqlite. We recently converted to postgresql 9.3 in an attempt to resolve the issue as suggested in prior posts. Despite switching to postgresql we continue to have these errors. Does anyone have any additional suggestions that may resolve this issue?

Thanks,

Todd

Traceback (most recent call last):

File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 122, in prepare_job

job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs )

File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 172, in build_command_line

work_dir_outputs = self.get_work_dir_outputs( job_wrapper )

File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 222, in get_work_dir_outputs

for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 168, in __get__

return self.impl.get(instance_state(instance),dict_)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 453, in get

value = self.callable_(state, passive)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 508, in _load_for_state

return self._emit_lazyload(session, state, ident_key)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 574, in _emit_lazyload

result = q.all()

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2115, in all

return list(self)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2227, in __iter__

return self._execute_and_instances(context)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances

result = conn.execute(querycontext.statement, self._params)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute

params)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement

compiled_sql, distilled_params

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context

context)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context

context)

File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute

cursor.execute(statement, parameters)

OperationalError: (OperationalError) database is locked u'SELECT library_dataset_dataset_association.id AS library_dataset_dataset_association_id,

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