Many thanks for your help. Your are right about database (I'm using SQLite). I've found a tutorial at GMOD (http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work with PostgreSQL, but can I change the current database to PostgreSQL without missing my datasets? I am running a single-user galaxy instance. Cheers, Milad
> Date: Wed, 12 Mar 2014 09:07:00 +0100 > From: h...@fmi.ch > To: mi.bast...@live.com > CC: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] error in workflow > > Hi Milad > > The error message: "database is locked" might be a hint. > > Are you using a PostgreSQL database or just SQLite ? If the latter, you > will often run in troubles when running more than one job at a time, due > to file locking. > > Regards, Hans-Rudolf > > > On 03/11/2014 07:41 PM, Milad Bastami wrote: > > Dear Galaxy Developers, > > I'm running galaxy local on ubuntu and trying to run a workflow on > > multiple datasets (separately). Occasionally when I try to run workflow > > on input dataset I get "Unable to finish job" error in some steps, in > > most time the problem will be solved when I run the workflow again, but > > this going to happen more frequently. I attached the error message here. > > I suspect it may be related to increase in number of datasets of the > > current history (1757 datasets with ~350GB size). > > I will appreciate your help > > > > Traceback (most recent call last): > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", > > line 116, in queue_job > > job_wrapper.finish( stdout, stderr, exit_code ) > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", > > line 1068, in finish > > self.sa_session.flush() > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", > > line 114, in do > > return getattr(self.registry(), name)(*args, **kwargs) > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", > > line 1718, in flush > > self._flush(objects) > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", > > line 1804, in _flush > > transaction.commit() > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", > > line 365, in commit > > t[1].commit() > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 2045, in commit > > self._do_commit() > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 2075, in _do_commit > > self.connection._commit_impl() > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1280, in _commit_impl > > self._handle_dbapi_exception(e, None, None, None, None) > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1277, in _commit_impl > > self.engine.dialect.do_commit(self.connection) > > File > > "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", > > line 307, in do_commit > > connection.commit() > > OperationalError: (OperationalError) database is locked None None > > > > > > > > ___________________________________________________________ > > 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/ > >
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