"An error occurred setting the metadata for this dataset"

Question: "An error occurred setting the metadata for this dataset"

16 months ago by

eurioste • 40 wrote:

Hello, I'm just reporting I'm getting "An error occurred setting the metadata for this dataset" for almost all jobs, including simple jobs that previously worked with the data in my workflow, like FastQ groomer jobs. Because of this many jobs are getting stalled or having errors.

software error metadata • 1.2k views

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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by eurioste • 40

I also have jobs just spinning or waiting. I think there's some trouble going on - you're not alone.

ADD REPLY • link written 16 months ago by louisa.pyle • 10

I'm also having this same or very similar error message with with programs like FASTQC and Trimmomatic. I have workflows I've used repeatedly in the past quite successfully - now they're failing but it seems that random steps in the process are failing. For example, one workflow has two FASTQC steps - somtimes one fails, sometimes both fail but the fact that sometimes one or the other succeeds tells me the problem isn't in my data but in the processing.

ADD REPLY • link modified 16 months ago • written 16 months ago by zachary.gaber • 80

Hello - We would like to track down this problem. Would one of you be able to send in a shared history link with the problematic datasets left intact?

Generate the history share link and include it in an email to galaxy-bugs@lists.galaxyproject.org (private list). Note the dataset numbers for input/output and also please include a link to this post so we can associate the two. How to generate a history share link: https://galaxyproject.org/learn/share/

Thanks for reporting the problems and our admin will look at this ASAP! Jen, Galaxy team

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen! email sent just now. Louisa

ADD REPLY • link written 16 months ago by louisa.pyle • 10

Thanks Louisa! We believe we know what is going on, fixed the problem, and I am going to post a reply. I'll update if reviewing your history changes anything.

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer, I did what you asked and sent an email containing links to this thread and my shared history with the bug. It's been happening very consistently (more than 75% of the time I try to run these operations I get a bug) for me for at least the past 24 hours so hopefully you guys won't have trouble reproducing the bug and then figuring out what's going on. Thanks for your help and please contact me if you need any information beyond what I put in the email!

Zachary

ADD REPLY • link written 16 months ago by zachary.gaber • 80

Thanks Zachary for sending this in. I will also look at your history to make sure more is not going on, however also try the advice below now as it is the most likely problem/resolution. Thanks! Jen

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer - I just reran the same workflow on the same data that's been getting bugged - seems to work now! Thanks for fixing this!

ADD REPLY • link written 16 months ago by zachary.gaber • 80

Oh, great news! Thanks for the update!

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello all

If you have had job execution problems at Galaxy Main (http:/usegalaxy.org) over the last few days, please do the following:

For successful jobs with metadata problems: Click on the "autodetect metadata" link within the expanded dataset box to reset. These datasets should be fully intact. However, rerunning is also an option.

For jobs that failed, these will have an error similar to: IOError: [Errno 2] No such file or directory: '/galaxy-repl/main/scratch2/XXXX' or Remote job server indicated a problem running or monitoring this job. Rerun the just jobs that failed or the complete workflow, your choice.

Note: If the job errors again with the Remote job server error, the problem could be with your inputs or tool form usage. Troubleshooting help is here. If you cannot determine the problem after reviewing, a bug report can be sent in.

For either: If a workflow was used and the history is complicated with success, failed, and metadata-problem jobs, permanently deleting the prior run and rerunning from the start may be the simplest solution.

Many will be rerunning jobs, so the queues may be longer than normal for certain job types. Please be patient and allow queued jobs to stay queued until executed.

Thanks for reporting the issues and please let us know if the reruns are problematic in this same post as a comment to this reply.

Jen, Galaxy team

ADD COMMENT • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks so much Jen and Galaxy team! Foolishly, I started with my longest job, so it's still running. We'll see!

ADD REPLY • link written 16 months ago by louisa.pyle • 10

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