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_paramsFile "/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,
PAML EMAIL DISCLAIMER: Information contained in this message may be privileged and confidential. If the reader of this message is not the intended recipient, be notified that any dissemination, distribution or copying of this communication is strictly prohibited. If this communication is received in error, please notify the sender immediately by replying to the message and deleting from your computer. Thank you
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/