Jobs running or queued for more than 48 hours

[Maddy-UW]

Hi there,

I have been trying to run some tools - FastQC, Trimmomatic, and CRISPResso2 from the usegalaxy.be server. FastQC jobs have been either running or queued since last Friday (~144 hours), Trimmomatic jobs have been queued since last Saturday (~120 hours), and CRISPResso2 jobs have been queued for ~24 hours.

Could someone please help me troubleshoot this?

Thank you!

[daniel_n578]

I am also experiencing the same issues.

[jennaj]

@Maddy-UW

usegalaxy.be

Hi @daniel_n578 and @Maddy-UW

I see a message on the server about planned downtime but do not know of the current status. I’ve sent a message through the web form to the server admins. You both could do the same. Find this on the server homepage (click on the upper top left icon, then scroll down a bit).

Let’s also ping them here. Hi @padge would you be able to let us know if anything special is going on right now on the server?

While we wait for feedback, the best general advice I have is to leave the jobs queued. If you delete and rerun, that only places the jobs back at the very end of the queue. This can significantly extend wait time, and if done often enough, a job may never get the chance to execute.

This guide does not list UseGalaxy.be yet, but probably should, and the same processing guidelines do apply.

@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-orange) 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).

---

Thanks for letting us know about the delays! More soon after the BE team reads the messages in their time zone! If either or both of you want to share a history with the queued jobs, we can help to double check that all of the inputs are in a good usable state (now), and the BE admins might be able to check for your specific tools/versions when they reply (later).

[Maddy-UW]

Hi @jennaj,

Thank you so very much for your response!
Just an update: Trimmomatic and CRISPResso2 are running smoothly now

FastQC is still taking a long time to run from the usegalaxy.be server but runs fine from the usegalaxy.org server.

Thank you again

[B0r1sD]

Hi all

Thank you for reporting this. We had to delete stuck FastQC jobs yesterday as they were the ones keeping your jobs in queue.

We are in the process of identifying the issue with FastQC; it is our top priority today. We will give an update as soon as it is fixed.

Your non-FastQC jobs should have run since.

Apologies for the inconvenience!

Kind regards
Boris from useGalaxy.be

[B0r1sD]

The problem has been identified (by @padge) and is getting fixed as we speak. An update will be officially communicated on the useGalaxy.be frontpage.