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,


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/

Reply via email to