# Fastq files not uploading
**URL:** https://help.galaxyproject.org/t/fastq-files-not-uploading/16484
**Category:** usegalaxy.eu support
**Tags:** upload
**Created:** [November 10, 2025, 8:22pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484 "2025-11-10T20:22:14Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 10, 2025, 8:22pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/1 "2025-11-10T20:22:15Z")
Fastq files have not uploaded for the past couple of hours, but no outage indicated on the status page.
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [November 10, 2025, 9:00pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/2 "2025-11-10T21:00:22Z")
Hi @imperialadmiral121
How are you loading data up to the [UseGalaxy.eu](http://UseGalaxy.eu) server? FTP, URL, local file?
Let’s start there, thanks! 🙂
XRef → [Getting Data into Galaxy](https://help.galaxyproject.org/t/getting-data-into-galaxy/10868)
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 10, 2025, 9:18pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/3 "2025-11-10T21:18:55Z")
Hi, I am uploading local files
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 10, 2025, 9:21pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/4 "2025-11-10T21:21:51Z")
It looks like some of the jobs that were stuck processing have started completing just now. I will monitor and update
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [November 10, 2025, 9:32pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/5 "2025-11-10T21:32:33Z")
Ok, great! 🚀
Yes, I ran a test and it completed quickly. Very small files but the queue should work the same for large or small.
- [https://usegalaxy.eu/u/jenj/h/test-upload-2025-11-10](https://usegalaxy.eu/u/jenj/h/test-upload-2025-11-10)
In general how the job queue works is below. Everyone has some set of concurrent “jobs” allowed. This means for a larger batch of data loading _or_ tool runs, some may run and complete before the others. Leaving items queued is the important part.
> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> ⏰ When working at [UseGalaxy.org](http://UseGalaxy.org), [UseGalaxy.eu](http://UseGalaxy.eu), or [UseGalaxy.org.au](http://UseGalaxy.org.au), your analysis jobs execute [at large scale academic clusters](https://training.galaxyproject.org/training-material/faqs/galaxy/#analysis). Hundreds of thousands of jobs process each month!
>
> - Use a [Workflow](https://training.galaxyproject.org/training-material/search2?query=workflow) for batch work.
> - Allow [queued (grey color) and executing (yellow-orange) datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_job_status.html) 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](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_jobs_not_running.html) (especially for ‘big’ jobs, e.g. alignments).
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 11, 2025, 2:28am UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/6 "2025-11-11T02:28:44Z")
I am able to run already-uploaded files, but the processing of uploaded files seems to have stopped working for me (even with a small test file uploaded using a different device remains gray). I will check again tomorrow
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 11, 2025, 3:56pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/7 "2025-11-11T15:56:46Z")
Update: no progress overnight. I tried uploading the small test file on the [usegalaxy.org](http://usegalaxy.org) server, and it was slower than normal but completed after ~5min.
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [November 11, 2025, 5:44pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/8 "2025-11-11T17:44:14Z")
Hi @imperialadmiral121
I’m glad you were able to load to the [UseGalaxy.org](http://UseGalaxy.org) server as a work-around!
The [UseGalaxy.eu](http://UseGalaxy.eu) server just seems to be busy. I see many unscheduled and queued jobs for the Upload tool – named DATA FETCH in these graphs.
Where → [How to see the UseGalaxy.eu job queue statistics](https://help.galaxyproject.org/t/how-to-see-the-usegalaxy-eu-job-queue-statistics/11837)
* * *
The best advice we can give is to get your data queued then allow it to process. For local data, you’ll need to stay connected. For cloud data, this will process while you are away. The same is true when it comes time to download the results, too.
Hope this helps! The EU administrators are watching what we are talking about here and will jump in if there is anything special to report. 🙂
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 11, 2025, 7:05pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/9 "2025-11-11T19:05:37Z")
Thanks for the info!
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 12, 2025, 4:22pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/10 "2025-11-12T16:22:50Z")
Update: [usegalaxy.eu](http://usegalaxy.eu) server uploads still not processing for me. Tried creating new histories, and switching between short-term and long-term storage. [usegalaxy.org](http://usegalaxy.org) is working fine.
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [November 12, 2025, 5:13pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/11 "2025-11-12T17:13:48Z")
Update: working again. One file did not upload correctly due to “bus error (core dumped),” but everything else is processing.
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [November 12, 2025, 5:58pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/12 "2025-11-12T17:58:12Z")
Thanks for the updates @imperialadmiral121 and I’m glad the ORG server is working for you.
Let’s ping the EU admins. Maybe they can provide more context. @wm75 – is there anything special going on or do you have any advice to add? Thanks!
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### Author:  [@wm75](https://help.galaxyproject.org/u/wm75)
#### Post date: [November 12, 2025, 7:34pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/13 "2025-11-12T19:34:13Z")
Well, we definitely had recurring upload issues on Galaxy Europe since the weekend.
Things are currently working and we hope it stays that way now.
Sorry for the inconvenience this has caused you,
Wolfgang
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [January 13, 2026, 11:55pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/14 "2026-01-13T23:55:00Z")
I seem to be having the same kind of issue with [usegalaxy.eu](http://usegalaxy.eu) today. [usegalaxy.org](http://usegalaxy.org) is working fine
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [January 14, 2026, 2:50am UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/15 "2026-01-14T02:50:32Z")
The files that were in progress (orange) have still not resolved, but the files that were still waiting to run (grey) have now completed (including the in-progress files that I re-queued).
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### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [January 24, 2026, 12:02am UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/16 "2026-01-24T00:02:51Z")
Hi @imperialadmiral121
How are your Upload jobs now?
The [UseGalaxy.org](http://UseGalaxy.org) server had some maintenance downtime in early January, but not last week. If you have some data that has been queued for “too long” at [UseGalaxy.org](http://UseGalaxy.org) I would be interested in looking at it. [Shared history link? Screenshot?](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469) If you include your username and history name in the screenshot, I can take a peek into the other details directly and provide some feedback.
Please let us know! Thanks! 🙂
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [January 25, 2026, 4:19pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/17 "2026-01-25T16:19:15Z")
The [usegalaxy.org](http://usegalaxy.org) server was working fine; I was having issues with the [usegalaxy.eu](http://usegalaxy.eu) server. I believe that I ended up deleting the in-progress files that had not resolved (as the re-queued files had already completed). Thanks for following up
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### Author:  [@Gabriel](https://help.galaxyproject.org/u/Gabriel)
#### Post date: [January 26, 2026, 11:00am UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/18 "2026-01-26T11:00:09Z")
Hello !
First of all, sorry for the issues caused using EU instance. We are currently facing some problems regarding our htcondor runner. We are not quiet sure yet what the root cause is and how we can fixed.
Some of the jobs could indeed stay in orange (queued) state and do not finish. This is quiet random and we cannot predict witch jobs will stay in this “state”. Internally, the condor queue finished the job, but the handler doesn’t pick up on it. For now we can force a restart on handlers
We are working on a solution and hope to fix this soon as possible. Thanks for reporting the issue!
Gabriel
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### Author:  [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)
#### Post date: [January 26, 2026, 5:16pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/19 "2026-01-26T17:16:59Z")
Thanks for the explanation!
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### Author:  [@Gabriel](https://help.galaxyproject.org/u/Gabriel)
#### Post date: [February 3, 2026, 8:22am UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484/20 "2026-02-03T08:22:29Z")
This should be mostly fixed since some days ago. Hope your jobs are not staying orange anymore 🙂
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