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 helpTraceback (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/
