Hi all, I have a client who is trying to run velvet on a small bacterial assembly in Galaxy. She is using our Core's custom Galaxy in the Amazon Cloud. It has had very few problems and we have been updating it and using it for years. However, after her assembly ran for a while, Galaxy crashed and now gives this error whenever you try to access it: Error Traceback: ⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110] URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request view body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:509 in logout view trans.handle_user_logout( logout_all=logout_all ) Module galaxy.web.framework:713 in handle_user_logout view self.sa_session.flush() Module sqlalchemy.orm.scoping:127 in do view return getattr(self.registry(), name)(*args, **kwargs) Module sqlalchemy.orm.session:1356 in flush view self._flush(objects) Module sqlalchemy.orm.session:1434 in _flush view flush_context.execute() Module sqlalchemy.orm.unitofwork:261 in execute view UOWExecutor().execute(self, tasks) Module sqlalchemy.orm.unitofwork:753 in execute view self.execute_save_steps(trans, task) Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view self.save_objects(trans, task) Module sqlalchemy.orm.unitofwork:759 in save_objects view task.mapper._save_obj(task.polymorphic_tosave_objects, trans) Module sqlalchemy.orm.mapper:1413 in _save_obj view c = connection.execute(statement.values(value_params), params) Module sqlalchemy.engine.base:824 in execute view return Connection.executors[c](self, object, multiparams, params) Module sqlalchemy.engine.base:874 in _execute_clauseelement view return self.__execute_context(context) Module sqlalchemy.engine.base:896 in __execute_context view self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) Module sqlalchemy.engine.base:950 in _cursor_execute view self._handle_dbapi_exception(e, statement, parameters, cursor, context) Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17 18:22:49.991937', 0, 110]
I will be getting more information from her soon, but I just wanted to post this to see if anybody had any suggestions about what might be going on and perhaps how to fix it? Any help would be highly appreciated. Thanks! - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
Hi Nik, I'm not sure if this is your case but it happened something similar to our Galaxy instance when I upgraded the postgresql server. I solved simply restarting Galaxy. F. Il 22/10/13 09.05, Nikhil Joshi ha scritto:
Hi all,
I have a client who is trying to run velvet on a small bacterial assembly in Galaxy. She is using our Core's custom Galaxy in the Amazon Cloud. It has had very few problems and we have been updating it and using it for years. However, after her assembly ran for a while, Galaxy crashed and now gives this error whenever you try to access it:
Error Traceback: ⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id <http://galaxy_session.id> = ?' ['2013-10-17 18:22:49.991937', 0, 110] URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request view body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:509 in logout view trans.handle_user_logout( logout_all=logout_all ) Module galaxy.web.framework:713 in handle_user_logout view self.sa_session.flush() Module sqlalchemy.orm.scoping:127 in do view return getattr(self.registry(), name)(*args, **kwargs) Module sqlalchemy.orm.session:1356 in flush view self._flush(objects) Module sqlalchemy.orm.session:1434 in _flush view flush_context.execute() Module sqlalchemy.orm.unitofwork:261 in execute view UOWExecutor().execute(self, tasks) Module sqlalchemy.orm.unitofwork:753 in execute view self.execute_save_steps(trans, task) Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view self.save_objects(trans, task) Module sqlalchemy.orm.unitofwork:759 in save_objects view task.mapper._save_obj(task.polymorphic_tosave_objects, trans) Module sqlalchemy.orm.mapper:1413 in _save_obj view c = connection.execute(statement.values(value_params), params) Module sqlalchemy.engine.base:824 in execute view return Connection.executors[c](self, object, multiparams, params) Module sqlalchemy.engine.base:874 in _execute_clauseelement view return self.__execute_context(context) Module sqlalchemy.engine.base:896 in __execute_context view self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) Module sqlalchemy.engine.base:950 in _cursor_execute view self._handle_dbapi_exception(e, statement, parameters, cursor, context) Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id <http://galaxy_session.id> = ?' ['2013-10-17 18:22:49.991937', 0, 110]
I will be getting more information from her soon, but I just wanted to post this to see if anybody had any suggestions about what might be going on and perhaps how to fix it? Any help would be highly appreciated. Thanks!
- Nik.
-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
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-- ============================================ Federico Zambelli, Ph.D. Bioinformatics, Evolution and Comparative Genomics Lab Dept. of Biosciences University of Milano - Italy What can be asserted without proof can be dismissed without proof. ============================================
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Federico Zambelli -
Nikhil Joshi