galaxy is not running

Hi, I am a beginner in run Galaxy. Starting from this morning, my galaxy stopped to run, the jobs in the history say “this job is waiting to run” and this status has last for a couple of hours. Anyone can tell me what I can do? I appreciate your help.


Dear @junnan.fang,
If you are a beginner with galaxy then please have a look at the training material for a Galaxy introduction Galaxy Training!.

Your question, depends on the galaxy instance you are working with. If you are working with or .org, then try to refresh your history, or resubmit your job.

Have a good day and best wishes,

1 Like

Hi @junnan.fang has a banner up explaining how the server resources will be allocated over the upcoming week (and why).

Jobs are expected to queue even when there is not an event going on. If the jobs do not move from queued (gray) to execute (yellow) after 72 hours, then a rerun may help. Just be aware that this removes the original job from the queue, and places the new job back at the end of the queue. If a server is busy, and many are, a rerun will result in even longer delays – or possibly never running if you keep deleting/rerunning before the jobs have a chance to be deployed to an executing stage.

FAQ: How Jobs Execute

I also added a tag to your post that points to similar Q&A about the subject. In short, job queue times at public servers depend on a few factors: how busy the server is, how many concurrent jobs you have running (queued + executing), what kinds of tools are you running (some tools require more resources, and those cluster nodes are the busiest), … and special factors noted in banners (events, downtime, known server issues).

For right now, I’d suggest leaving the job as it is, to give it some time to move through the queue. Or you can rerun as @Flow suggests, as it sounds like it hasn’t been that long since you started it up and there was a small issue at earlier today – although that resulted in job failures that required a rerun (resource allocation issues) – not jobs stalling in queued status (what it seems your situation is).

The choice is yours on how to proceed :slight_smile:

ps: For anyone participating in the GCC2021 training event, special queues will be set up to prioritize your tutorial work once the event starts. These particular queues will only be available to registered students and will have resources appropriate for training-sized data only (larger work will fail for resource reasons). Your event instructions will describe how to join these queues, and you can contact your instructors in Slack should you need more help. Non-event end-users will have their jobs sent the regular queues the servers support, and some may have extended queue times and related resource allocation changes – if those are in place, the server will note so in their banner.

2 posts were split to a new topic: Question about visualization tool: Finich