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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