Workflow jobs not running/queueing on a local Galaxy version 17.09

Question: Workflow jobs not running/queueing on a local Galaxy version 17.09

10 months ago by

TWV • 20

TWV • 20 wrote:

As has been reported earlier on (amongs others) these threads:

The most recent of which dates back 3 months ago, I have the issue that sometimes when running a workflow I get the notification telling me:

Successfully invoked workflow #WORKFLOWNAME. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.

However no jobs are loaded and nothing happens after refreshing nor are the jobs ran in another history. The jobs do also not appear in the admin "Jobs" pannel.

Restarting the server altogether seems to somehow fix the problem (sometimes, and only temporarily).

I am using a local galaxy installation.

Thanks in advance for your support.

queue workflow job local • 815 views

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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by TWV • 20

Hello,

The prior issues were due to a problem with the job handler on the public Galaxy main server at https://usegalaxy.org. It was corrected. Ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/47

To start the troubleshooting for your issue, more details would help:

what is the build/version of your local?
is there a cluster in use? have you checked your own job handlers?
workflows always had the problem or is this new behavior?
have there been any admin changes between the time workflows functioned and now?
do the tools in the workflow run when executed outside of the workflow?

ADD REPLY • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k

The build version is 17.09 as found through /api/version
The local galaxy is being run on a single PC
The local galaxy is a recent instance, therefore it's hard for me to say whether the problem existed from the start but didn't manifest right away. But I think it is new behaviour
I have installed new tools from the toolshed, changed the local data, and managed user groups
While currently the workflow jobs invoke properly, and I thus cannot verify your request, I recall having to manually perform the various steps. Thus the tools do work.

This issue occurs several times a day, but I can't seem to make it occur purposefully.

ADD REPLY • link modified 10 months ago • written 10 months ago by TWV • 20

Thank you for the details. Others have reported similar problems recently when using 17.09. Our team is looking into why this is occurring. More feedback soon.

Some of the discussion can be found in this chat channel: https://gitter.im/galaxyproject/Lobby

And there are recently opened workflow issues here (there will likely be more as we figure out what the root issue is): galaxyproject/galaxy/issues

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

Do you see reoccurring messages in your log about a delayed workflows invocation?

ADD REPLY • link written 10 months ago by Bjoern Gruening ♦ 5.1k

Searching for "Delay" did not return any hits in the log file

ADD REPLY • link written 10 months ago by TWV • 20

Hard to tell then, can you attach a log file for the entire process from launching the job onward. Do you use multiple handlers? An external scheduler?

ADD REPLY • link written 10 months ago by Bjoern Gruening ♦ 5.1k

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