The job is finished..but not in the history
hi, I'm writing some wrappers to connect galaxy with some scripts/programs. I can't understand why, for some, the job in the history never end. Here an example of the log output <output> 127.0.0.1 - - [20/Aug/2010:14:18:38 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" galaxy.jobs DEBUG 2010-08-20 14:18:41,524 job 81 dispatched galaxy.jobs.runners.local DEBUG 2010-08-20 14:18:41,694 executing: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20 127.0.0.1 - - [20/Aug/2010:14:18:42 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" 127.0.0.1 - - [20/Aug/2010:14:18:46 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... 127.0.0.1 - - [20/Aug/2010:14:19:18 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" galaxy.jobs.runners.local DEBUG 2010-08-20 14:19:20,831 execution finished: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20 127.0.0.1 - - [20/Aug/2010:14:19:22 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" 127.0.0.1 - - [20/Aug/2010:14:19:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... and so on </output> If i check the "running" dataset clicking the eye i see the final result that I expect.... Then, checking in the table 'dataset' (in universe.sqlite) i obtain 87|running why the flag isn't changed to ok? any ideas? Tnx :) raf
amerite wrote:
hi, I'm writing some wrappers to connect galaxy with some scripts/programs. I can't understand why, for some, the job in the history never end.
Hi Raf, It looks like the job is probably setting metadata on the output dataset. How big is this output and how long have you waited? You may also want to try setting: set_metadata_externally = True in universe_wsgi.ini. Thanks, --nate
Here an example of the log output
<output> 127.0.0.1 - - [20/Aug/2010:14:18:38 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
galaxy.jobs DEBUG 2010-08-20 14:18:41,524 job 81 dispatched
galaxy.jobs.runners.local DEBUG 2010-08-20 14:18:41,694 executing: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20
127.0.0.1 - - [20/Aug/2010:14:18:42 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
127.0.0.1 - - [20/Aug/2010:14:18:46 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... 127.0.0.1 - - [20/Aug/2010:14:19:18 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
galaxy.jobs.runners.local DEBUG 2010-08-20 14:19:20,831 execution finished: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20
127.0.0.1 - - [20/Aug/2010:14:19:22 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
127.0.0.1 - - [20/Aug/2010:14:19:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... and so on </output>
If i check the "running" dataset clicking the eye i see the final result that I expect.... Then, checking in the table 'dataset' (in universe.sqlite) i obtain
87|running
why the flag isn't changed to ok? any ideas? Tnx :) raf _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
hi, I'm writing some wrappers to connect galaxy with some scripts/programs. I can't understand why, for some, the job in the history never end.
Hi Raf,
It looks like the job is probably setting metadata on the output dataset. How big is this output and how long have you waited? You may also want to try setting:
set_metadata_externally = True
in universe_wsgi.ini.
Thanks, --nate
Yes, the job produces a big file...some GB; I don't know how long it takes because after 5 hours I've stopped the task. You are right, setting metadata in separate processes makes the process responsive... Thank you!!!! :) raf
participants (2)
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amerite -
Nate Coraor