Question: Workflow jobs not running/queueing on a local Galaxy version 17.09
0
gravatar for TWV
4 months ago by
TWV20
TWV20 wrote:

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

  1. https://biostar.usegalaxy.org/p/25048/
  2. https://biostar.usegalaxy.org/p/21125/
  3. https://biostar.usegalaxy.org/p/21100/
  4. https://biostar.usegalaxy.org/p/21084/

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 • 363 views
ADD COMMENTlink modified 8 weeks ago by Jennifer Hillman Jackson25k • written 4 months ago by TWV20

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 REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k
  • 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 REPLYlink modified 4 months ago • written 4 months ago by TWV20
1

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 REPLYlink written 4 months ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 4 months ago by Bjoern Gruening5.0k

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

ADD REPLYlink written 4 months ago by TWV20
1

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 REPLYlink written 4 months ago by Bjoern Gruening5.0k
0
gravatar for Jennifer Hillman Jackson
8 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Update: Galaxy is now at version 18.01 which may have addressed the issue. Closing.

ADD COMMENTlink written 8 weeks ago by Jennifer Hillman Jackson25k
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