4:11 p.m.
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(a)glbrc.wisc.edu
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--
Jennifer Jackson
http://usegalaxy.org