> Date: Wed, 12 Mar 2014 09:07:00 +0100
> From: hrh@fmi.ch
> To: mi.bastami@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
> >
> >
> >
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