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__.p y", line 42, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 120, in __init__ self.__check_jobs_at_startup() File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", 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__.p y", 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/lo cal.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__.p y", 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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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/SQLA lchemy-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 De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.