# AGAT convert\_GTF2GFF job keeps running **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** troubleshooting\ **Created:** [February 16, 2024, 7:49am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722 "2024-02-16T07:49:57Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 16, 2024, 7:49am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/1 "2024-02-16T07:49:57Z")
Hello, I have started a GTF6GFF conversion job using GTF data created by Braker3 on Galaxy, This job runs now for ca. 24 hrs, but did not complete. Before cancelling the job, is there any possibility to find out, why this job did not complete? UUID 3aec77c2-c6d0-43d2-a203-a6580bc33481 standard output and standard error are empty. Best, ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 19, 2024, 6:58pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/2 "2024-02-19T18:58:15Z")
Hi @ARW-UBT I’m not sure what you mean by “did not complete”. If a job is still running, the logs are not written back yet. Maybe this helps? > [@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) 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). ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 20, 2024, 7:52am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/3 "2024-02-20T07:52:19Z")
@jennaj Correct! But a GTF to GFF3 conversion jobs should complete within seconds and not run for 4 days. Even if my job is somewheren in the queue, I would expect to complete within a reasonable time. Would you mind to look at the job itself or forward this issue to some sys admin? Best, ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 20, 2024, 7:00pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/4 "2024-02-20T19:00:36Z")
Hi @ARW-UBT > [@ARW-UBT](#): > > Would you mind to look at the job itself or forward this issue to some sys admin? Sure. You can share the history with the job that is currently running and I’ll check. See the banner at the top of the forum for the how-to, or see [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469). This will need a history share link, not just screenshots. ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 21, 2024, 6:42am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/5 "2024-02-21T06:42:13Z")
@jennaj Sure, here is the link. Could not find your email address or user account to share the link, so I have to make it public here… > **[Galaxy](https://usegalaxy.eu/published/history?id=871e3be804edeb6d)** > > Galaxy is a community-driven web-based analysis platform for life science research. Best, ---
**Author:** ![Jacques\_Dainat](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jacques_dainat/32/5244_2.png) [@Jacques\_Dainat](https://help.galaxyproject.org/u/Jacques_Dainat)\ **Post date:** [February 21, 2024, 8:28am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/6 "2024-02-21T08:28:52Z")
Hi, An old version of that script was bugged. Would it be possible to know which version of agat is in use? ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 21, 2024, 8:55am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/7 "2024-02-21T08:55:38Z")
According to the info from Job Dependencies: agat v1.2.0 ---
**Author:** ![Jacques\_Dainat](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jacques_dainat/32/5244_2.png) [@Jacques\_Dainat](https://help.galaxyproject.org/u/Jacques_Dainat)\ **Post date:** [February 21, 2024, 10:21am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/8 "2024-02-21T10:21:23Z")
If you don’t mind to share you braker3 file (via GitHub issue here [Issues · NBISweden/AGAT · GitHub](https://github.com/NBISweden/AGAT/issues) or by mail) I may have a look to see AGAT’s performance on its own (outside of Galaxy) ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 21, 2024, 1:22pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/9 "2024-02-21T13:22:02Z")
@Jacques_Dainat Just uploaded the braker3 output as zipped file to github. Best, ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 21, 2024, 3:59pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/10 "2024-02-21T15:59:38Z")
ok, I killed the job at Galaxy, as this is not an AGAT bug. Best, ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 21, 2024, 6:00pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/11 "2024-02-21T18:00:54Z")
Hi @ARW-UBT It looks like standardizing the fasta file was enough. Or did I not understand the data? Some tools assume that everything on the \> lines is the “identifier”. Removing everything after the first whitespace can be done with **NormalizeFasta** to adjust the data directly in Galaxy next time. Always worth a try to do that when an error comes up: different tools, different authors, different data assumptions. Sometimes the Galaxy wrapper around a tool can do the adjustment but not always possible. I guess you could report this to the author at that same repository as an enhancement request for some future release. Considering just the first “word” on the fasta title line as the sequence identifier is a pretty universal standard, and data providers tend to put descriptions there (on purpose). And if it turns out that it is not the underlying tool’s requirement, but related to how the tool was wrapped for Galaxy, they could help us to adjust it. Would make the tool friendlier. XRef for others that run into something similar. This tool is not unique about the format assumption. Meaning, some tools can parse the identifiers out of a \> line fine, some cannot. Standardizing doesn’t hurt unless a tool is actually using the description content, and you’ll probably recognize the few cases when that is needed. → [FAQ: Working with very large fasta datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_working_with_fasta.html) ---
**Author:** ![ARW-UBT](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arw-ubt/32/4034_2.png) [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Post date:** [February 22, 2024, 7:24am UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/12 "2024-02-22T07:24:54Z")
Hi @jennaj It was the AGAT gtf2gff job, that did not complete, the Braker3 job was ok after removing description from the header lines. I could confirm the results by the AGAT developers, the gtf2gff conversion works on a standalone AGAT. Best, ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [July 16, 2025, 4:58pm UTC](https://help.galaxyproject.org/t/agat-convert-gtf2gff-job-keeps-running/11722/13 "2025-07-16T16:58:54Z")
Closed on July 16, 2025, 4:58pm UTC