Hi Freerk, It looks like you're using SQLite, possibly on NFS? This is not a very robust database for a multi-user installation, and I'd suggest switching to Postgres or MySQL. More details are on the Production Server page, here: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer Can you ensure that your database file (by default, database/universe.sqlite) can be opened by the command-line sqlite tool, and perform some basic queries? Is the database file writable by your Galaxy user? --nate Dijk, F van wrote:
Hi,
I have a problem with Galaxy which we're running locally. Somehow we overloaded Galaxy with the jobs which resulted in the database server going down. Now when I try to restart Galaxy the following error is displayed:
galaxy.jobs DEBUG 2010-02-08 17:14:08,705 recovering job 1050 in local runner Traceback (most recent call last): File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/app.py", line 67, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 42, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 120, in __init__ self.__check_jobs_at_startup() File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 148, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 785, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 179, in recover job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." )
File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 460, in change_state dataset.state = state File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 478, in set_dataset_state object_session( self ).flush() #flush here, because hda.flush() won't flush the Dataset object File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
self._flush(objects) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1434, in _flush
flush_context.execute() File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
UOWExecutor().execute(self, tasks) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
self.save_objects(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
c = connection.execute(statement.values(value_params), params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
return Connection.executors[c](self, object, multiparams, params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
return self.__execute_context(context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) unable to open database file u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2010-02-08 16:14:08.738227', 'error', 1084]
Do you know how to solve this problem? I hope to hear from you soon.
Regards,
Freerk van Dijk
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