Trimmomatic Job Stuck in Queue -- Extended job queue timing across public Galaxy servers

usegalaxy.org support
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Good evening, I had started a Trimmomatic job on a paired end dataset at about 1:10 UTC. It’s been nearly 3 hours now with the jobs stuck in queue. Are you currently experiencing a lot of traffic?
Another question I had was how many jobs I could run concurrently? I was going to queue FastQC as well, but I’m unsure if queuing too many jobs might lead to an error. I apologize if the questions were a little basic, I’ve just started using Galaxy. Thanks for your time!

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Hi @aramesh

Were the jobs queued (gray in color) when you wrote in? That means they were staged and will process as resources become available. After 4 days, those likely completed. All public Galaxy servers are very busy, not just usegalaxy.org.

All compute-intensive jobs are queuing longer than usual due to the high load on the servers and clusters. Jobs queuing for several days would not be unusual, and even then only a subset of jobs may run at a time. Avoid deleting and rerunning – that will only place the jobs back at the end of the queue again, further extending wait time.

Using workflows is a good way to ensure work proceeds at the fastest possible rate. The entire analysis is queued up and will run as resources become available, without intervention.

You can also queue up jobs directly. Having many queued jobs is fine. The work will generally execute in the order submitted – but some tools may route to a different cluster than others and run out of order (unless dependent on some upstream job to run). So yes, there are some limits on the number of concurrent jobs anyone will have “executing” (actually running then completing, not just queued) but what tools those are can also be a factor.

If you have urgent work, setting up your own Galaxy server is an option, too.

I added a few tags to your post that will link to other Q&A about all of this, including FAQs and resource links. But if you have a specific question that doesn’t seem to be addressed yet or anything is unclear, we can try to help more/clarify directly here.

Thanks!

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Thanks a lot for your response, and answering my questions @jennaj! The jobs were completed after a couple days like you said.

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