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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