Trim Galore running for days?

[krisslou]

I started trim galore on my data (collection of 72 files) a few days ago, and it’s stuck. 26 files have been processed and 1 has been “running” for more than 3 days…
how can I stop this? or skip this file and continue to the next one?

[jennaj]

Hi @krisslou

It sounds like your jobs are processing. Leaving your jobs queued is likely the best advice. You are working at a cluster that runs everyone’s jobs. Some of your jobs run, some of other people’s jobs run, more of yours, repeat.

I’m not sure what you mean by this:

@krisslou

how can I stop this? or skip this file and continue to the next one?

You can delete jobs if you don’t want them anymore. But if you delete them before they create inputs needed for a downstream tool, then you won’t have that input available anymore.

More help below. You can also click on this tag for prior Q&A queued-gray-datasets

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How jobs work →

@jennaj

When working at UseGalaxy.org, UseGalaxy.eu, or UseGalaxy.org.au, your analysis jobs execute at large scale academic clusters. Hundreds of thousands of jobs process each month!

• Use a Workflow for batch work.
• Allow queued (grey color) and executing (yellow) datasets to finish processing.
• Deleting and rerunning puts your job back at the end of the queue again!
• Job priority is the exactly the same for everyone.
• Be patient. Galaxy is a free service, when a lot of people are using it, you may have to wait longer than usual (especially for ‘big’ jobs, e.g. alignments).

Hope this helps!

[krisslou]

Thanks

is it normal that it’s stuck on the same file for a week?
the other files were processed a week ago.

[jennaj]

Hi @krisslou

You are working at UseGalaxy.org, correct? I can check the administration details at the server. Do you want to share the history? I’ll need to see the technical details for this. How to → FAQ: Sharing your History

You can post that link back here. Once we are done you can unshare.