3 day+ queue time for Trinity Assembly

usegalaxy.eu support
1

Hi Everyone,

I queued up a Trinity Assembly at Saturday Jan 13th 14:52:54 2024 GMT+13 but it is still sitting in ‘Job is waiting to run’. I ran a MultiQC job yesterday and that started processing immediately. I’ve seen other posts from posters with similar issues however, their complaints seem to be about it sitting in queues for 24 hours or less. Is there anything I need to do to check if it’s stuck? If this is just because the server is busy is there any way to estimate how much longer it will sit in the queue.

Thank you wonderful Galaxy team, I appreciate you making this lovely service available.

William

2

Hi @WilliamC

Your job has been continually queued for four days now? And the input datasets to that tool are green/ready to use?

If are you running a really large number of jobs, that might be possible. But if you are just running a few jobs, that seems unusual.

Xref: Troubleshooting resources for errors or unexpected results

Do this if you would like us to help more:

  1. Start up a rerun for the original job.
  2. Don’t delete that original! You want to keep your queue placement.
  3. Generate a share back a link to your history with the original and rerun job and we can try to help more. If you are not sure how, see that FAQ I linked above.

Different tools run on different clusters, and some clusters are busier that others. Why? Because they are already running computationally expensive jobs, they take longer to free up for new work. But things will run. Never delete and rerun in hopes that things will go quicker since the opposite will result!

Let’s start there :slight_smile:

3

Hi @jennaj

I am not sure I would have permission to share my history so here are some screen shots:

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image1294×848 66.3 KB

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All the inputs are green and ready to go. I have queued a rerun as well. Both the original and the newly queued jobs are waiting in queue.

If you need the history I can provide you access via email.

Thank you for your help.

4

All items in the timmomatic collection are green and complete.

5

I have previously run this assembly on the galaxy.org server over christmas and it took a total of 24 hours to queue and then process.

1 Like
6

Hi @WilliamC

The EU chat has some comments about longer wait times. Find the chat link at the bottom of the server homepage, or you can use this Matrix invitation https://matrix.to/#/!pTWTMgjwPzvoMkeBrf:gitter.im/$utXqhVBDXefRYQ-e3FuqPXtNcpkw4LSJdxWt3wLcLZc?via=gitter.im&via=matrix.org&via=matrix.clareira.net

So, the wait is not just for you, but everyone running larger tools. The best advice is to keep your jobs queued. You could let both sets run through to get a better idea about how long jobs are queuing for this tool right now, or delete the second set after the first finishes since timing is not always the same.