Question: debug warnings from delayed job(s) bloating log file
1
gravatar for jdv
20 days ago by
jdv30
jdv30 wrote:

On a local Galaxy instance, the main log is being filled with lines like this, printing every few seconds repeatedly:

galaxy.workflow.run DEBUG 2017-11-22 14:15:50,713 Marking step 10769 outputs of invocation 5849 delayed (dependent step [10768] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:50,714 Marking step 10770 outputs of invocation 5849 delayed (dependent step [10769] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:50,714 Marking step 10771 outputs of invocation 5849 delayed (dependent step [10768] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:51,895 Marking step 10760 outputs of invocation 5842 delayed (dependent collection [3034] not yet populated with datasets)
galaxy.workflow.run DEBUG 2017-11-22 14:15:51,895 Marking step 10761 outputs of invocation 5842 delayed (dependent step [10760] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:51,897 Marking step 10762 outputs of invocation 5842 delayed (dependent collection [3035] not yet populated with datasets)
galaxy.workflow.run DEBUG 2017-11-22 14:15:51,897 Marking step 10763 outputs of invocation 5842 delayed (dependent step [10762] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:52,033 Marking step 10760 outputs of invocation 5846 delayed (dependent collection [3058] not yet populated with datasets)
galaxy.workflow.run DEBUG 2017-11-22 14:15:52,034 Marking step 10761 outputs of invocation 5846 delayed (dependent step [10760] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:52,035 Marking step 10762 outputs of invocation 5846 delayed (dependent collection [3059] not yet populated with datasets)
galaxy.workflow.run DEBUG 2017-11-22 14:15:52,036 Marking step 10763 outputs of invocation 5846 delayed (dependent step [10762] delayed, so this step must be delayed)
galaxy.workflow.run DEBUG 2017-11-22 14:15:52,173 Marking step 10768 outputs of invocation 5849 delayed (dependent collection [3069] not yet populated with datasets)

As far as I can tell, there are no running jobs under any user, and I have painstakingly deleted all paused jobs littering old histories. However, the messages persist even after a restart. I just updated to 17.09 to see if that would fix the issue (I saw one relevant message on IRC suggesting such) but it did not.

Any advice on how to find and stop the rogue jobs would be appreciated.

admin galaxy debug log • 40 views
ADD COMMENTlink written 20 days ago by jdv30

Reference: issue discussion at https://gitter.im/galaxyproject/Lobby aka #galaxyproject IRC: https://botbot.me/freenode/galaxyproject/2017-10-24/

ADD REPLYlink written 1 hour ago by Jennifer Hillman Jackson23k
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