Hi Branden, If you have not done so, updating to the latest revision at bitbucket should solve the issue. Or, you can set track_jobs_in_database = True in your local instance. Hopefully this helps, Jen Galaxy team On 9/9/10 7:20 PM, Branden Timm wrote:

Hello, I seem to be having database-related issues when running my workflow.

galaxy.jobs DEBUG 2010-09-09 21:14:48,967 dispatching job 180 to local runner galaxy.jobs INFO 2010-09-09 21:14:49,058 job 180 dispatched galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:49,697 executing: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1 galaxy.jobs ERROR 2010-09-09 21:14:50,209 failure running job 181 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x1a4074d0>' is not persistent within this Session 146.151.211.150 - - [09/Sep/2010:21:14:48 -0500] "POST /workflow/run?id=f597429621d6eb2b HTTP/1.1" 200 - "http://galaxy.glbrc.wisc.edu/workflow/run?id=f597429621d6eb2b" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.17.8 (KHTML, like Gecko) Version/5.0.1 Safari/533.17.8" galaxy.jobs ERROR 2010-09-09 21:14:51,219 failure running job 182 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x2aaab001acd0>' is not persistent within this Session galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:52,460 execution finished: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1

In Galaxy itself, the SOAP tool returns its results and the rest of the jobs just wait to run. Why am I having these errors?

Cheers

-- Branden Timm btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

-- Jennifer Jackson http://usegalaxy.org