I guess I should pay more attention to previous posters-- The fix for me was to set

track_jobs_in_database = True

Apparently fixed in a recent revision. Sorry for the noise on the list.

-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587

On Thu, Sep 16, 2010 at 10:22 PM, Jacob Biesinger jake.biesinger@uci.eduwrote:

Hi! I have a pretty simple NGS workflow I've set up. I'm running Galaxy's MACS wrapper pushing the output to MEME, a motif finder, in hopes of finding overrepresented TF motifs.

Running MACS and then MEME when the job is complete works just fine, but when I extract the workflow or create my own workflow and link the pieces together, I get a strange SQLAlchemy persistence error when MACS is run. MACS successfully completes and I can see the output just fine, but the jobs that follow in the workflow stay grayed out forever. I can run other jobs just fine, so I don't think the dispatcher died. Here is the error message:

69.234.135.61 - - [16/Sep/2010:22:08:44 -0700] "GET /workflow/list_for_run HTTP/1.1" 200 - "http://iron.ics.uci.edu :8080/root/tool_menu" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.4; en-US; rv:1.9.0.4) Gecko/2008102920 Firefox/3 .0.4" 169.234.135.61 - - [16/Sep/2010:22:08:46 -0700] "GET /workflow/run?id=1cd8e2f6b131e891 HTTP/1.1" 200 - "http://iron. ics.uci.edu:8080/workflow/list_for_run" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.4; en-US; rv:1.9.0.4) Gecko/20 08102920 Firefox/3.0.4" galaxy.jobs DEBUG 2010-09-16 22:09:09,483 dispatching job 33 to local runner galaxy.jobs INFO 2010-09-16 22:09:09,725 job 33 dispatched galaxy.jobs.runners.local DEBUG 2010-09-16 22:09:10,159 executing: python /home/galaxy/galaxy_dist/tools/peak_callin g/macs_wrapper.py /home/galaxy/galaxy_dist/database/job_working_directory/33/tmpSvTS8S /home/galaxy/galaxy_dist/data base/files/000/dataset_84.dat /home/galaxy/galaxy_dist/database/files/000/dataset_87.dat /home/galaxy/galaxy_dist/da tabase/job_working_directory/33/dataset_87_files galaxy.jobs ERROR 2010-09-16 22:09:11,379 failure running job 34 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 186, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.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-py2.6.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-py2.6.egg/sqlalchemy/orm/session.py", line 1236, in _validate_persistent mapperutil.state_str(state)) InvalidRequestError: Instance '<Job at 0x5e04f90>' is not persistent within this Session galaxy.jobs ERROR 2010-09-16 22:09:11,925 failure running job 35 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 186, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.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-py2.6.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-py2.6.egg/sqlalchemy/orm/session.py", line 1236, in _validate_persistent mapperutil.state_str(state)) InvalidRequestError: Instance '<Job at 0x5e57d10>' is not persistent within this Session galaxy.jobs ERROR 2010-09-16 22:09:12,666 failure running job 36 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 186, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.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-py2.6.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-py2.6.egg/sqlalchemy/orm/session.py", line 1236, in _validate_persistent mapperutil.state_str(state)) InvalidRequestError: Instance '<Job at 0x5e4b350>' is not persistent within this Session 169.234.135.61 - - [16/Sep/2010:22:09:08 -0700] "POST /workflow/run?id=1cd8e2f6b131e891 HTTP/1.1" 200 - "http://iron .ics.uci.edu:8080/workflow/run?id=1cd8e2f6b131e891" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.4; en-US; rv:1.9.0 .4) Gecko/2008102920 Firefox/3.0.4" ... a few job failures later galaxy.jobs.runners.local DEBUG 2010-09-16 22:09:15,495 execution finished: python /home/galaxy/galaxy_dist/tools/pe ak_calling/macs_wrapper.py /home/galaxy/galaxy_dist/database/job_working_directory/33/tmpSvTS8S /home/galaxy/galaxy_ dist/database/files/000/dataset_84.dat /home/galaxy/galaxy_dist/database/files/000/dataset_87.dat /home/galaxy/galax y_dist/database/job_working_directory/33/dataset_87_files galaxy.jobs DEBUG 2010-09-16 22:09:16,192 job 33 ended

It seems that the subsequent jobs (34, 35, etc) aren't waiting for MACS to complete.

FYI: Running fairly recent checkout of galaxy_dist (not more than a month old). Using Postgres 8.4.4 currently, but was on the default sqlite3 table schema, where I saw the same issue. Ubuntu 10.04, with BASH replacing the default DASH.

Any thoughts or places I could look to figure out what's going on?

-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587