Question: Stdout And Stderr Files
gravatar for Poornima Pochana
6.5 years ago by
Poornima Pochana20 wrote:
Hi, I have a personal galaxy instance with the runner as SGE. I am able to successfully submit jobs, and the output folder is created at $file_path. But I see that the SGE job log files ie., stdout and stderr - <job-name>.o and <job-name>.e are being removed in the cleanup function in Is this right? Is galaxy capturing the jobs stdout and stderr some where else? Also when I click on the link “Tool Standard Output” from galaxy web interface, it returns empty. Is there a setting that I should have to view jobs stdout, stderr from the web interface? Thanks, Poornima.
galaxy • 1.3k views
ADD COMMENTlink modified 6.5 years ago by Scott McManus130 • written 6.5 years ago by Poornima Pochana20
gravatar for Scott McManus
6.5 years ago by
Scott McManus130
Scott McManus130 wrote:
Yes, Galaxy stores the stdout and stderr in the database once the job is complete. The .o and .e files are automatically removed once this is complete. You should be able to click on the tool panel's (the panel on the righthand side) info button for each tool, which is what it appears you are doing. There shouldn't be anything that you have to set to see the stdout and stderr. Are you able to see output for other tools? -Scott
ADD COMMENTlink written 6.5 years ago by Scott McManus130
Thanks Scott. I did find them in the database in the table “job”. So far, the jobs that I ran - FastQ formatting and QA did not produce any stdout and stderr and thats why I couldn’t see any content by clicking on the info button, and database table also shows empty rows. I ran a FastQ trimmer job, which did produce stdout and I was able to see this from galaxy web interface by clicking on “Tool Standard Output” link and also in the database table. Another suggestion I got from local galaxy-dev was that, by enabling debugging (set "debug = True" in universe_wsgi.ini) .o and .e files are preserved in the $file_path and are not removed once the job is complete. Thanks, Poornima.
ADD REPLYlink written 6.5 years ago by Poornima Pochana20
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