# BUSCO Fatal error: Exit code 1 () **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-help, busco\ **Created:** [September 25, 2024, 1:18pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544 "2024-09-25T13:18:16Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![mmontonerin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mmontonerin/32/6122_2.png) [@mmontonerin](https://help.galaxyproject.org/u/mmontonerin)\ **Post date:** [September 25, 2024, 1:18pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/1 "2024-09-25T13:18:16Z")
I am trying to run BUSCO on different genome assemblies, but I keep getting the error: `Fatal error: Exit code 1 ()` The log doesn’t give any descriptive information of the problem: ```auto | 2024-09-25 15:08:55 ERROR:|Something went wrong. Results not recorded.| |---|---| |2024-09-25 15:08:55 ERROR:|BUSCO analysis failed!| |2024-09-25 15:08:55 ERROR:|Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues| ``` I have tried changing all the options, utilizing cache databases, downloading the libraries, selecting the lineage, allowing for auto-select lineage… I keep getting the same error again and again. The genome assemblies are of Pseudomonas bacteria. History: [Galaxy](https://usegalaxy.eu/u/mmontonerin/h/troubleshooting) I am using BUSCO on dataset 4 and 13. I have a group of students that should be able to run BUSCO in 2 days, so I hope to get this fixed as soon as possible. 😥 ---
**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:** [September 25, 2024, 4:50pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/2 "2024-09-25T16:50:46Z")
Welcome, @mmontonerin 🙂 Thank you for posting all of these details! Super helpful. I’m reviewing, more feedback soon. And, as a quick solution, I’m wondering if [using the prior version](https://training.galaxyproject.org/training-material/faqs/galaxy/tools_change_version.html) works. I’ll be testing that too but maybe gets you a quicker “fix”. ---
**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:** [September 26, 2024, 5:21pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/3 "2024-09-26T17:21:05Z")
HI @mmontonerin So … the BUSCO tool, when it doesn’t find any scientific result, will report the error that you had. When used on the command-line, maybe this message is clearer to the scientist using the tool, and when used in Galaxy, it looks a bit like a server side error, but this is actually just a result of “not found” (probably at the assembly step for your error). One solution is to try out different settings. You are already specifying a linage, which is great. Another item you can try is to use different “mode” settings. I ran some tests in my copy of your history, and labeled those with the tool version and which mode was set. Maybe this helps? [https://usegalaxy.eu/u/jenj/h/copy-of-troubleshooting-httpshelpgalaxyprojectorgtbusco-fatal-error-exit-code-113544](https://usegalaxy.eu/u/jenj/h/copy-of-troubleshooting-httpshelpgalaxyprojectorgtbusco-fatal-error-exit-code-113544) Let me know once you get a copy and I’ll delete that. Your data looks like it was sourced from a tutorial. If you think the tutorial had the wrong settings explained, please share back the link and I’ll review it if it was a [GTN tutorial](https://training.galaxyproject.org/). If the tutorial was from someone else, you should report the problem to them (or, they may recommend a specific version of BUSCO to replicate results). Hope this helps, and you can ask follow up questions. 🙂 ---
**Author:** ![mmontonerin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mmontonerin/32/6122_2.png) [@mmontonerin](https://help.galaxyproject.org/u/mmontonerin)\ **Post date:** [September 26, 2024, 5:33pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/4 "2024-09-26T17:33:46Z")
This was very helpful! Changing to version 5.5.0 worked perfectly 🙂 ---
**Author:** ![mmontonerin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mmontonerin/32/6122_2.png) [@mmontonerin](https://help.galaxyproject.org/u/mmontonerin)\ **Post date:** [September 27, 2024, 1:22pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/5 "2024-09-27T13:22:55Z")
Thanks for this reply and all the testing. I already copied it, so you can delete it from your side. The dataset is for a tutorial I have created for a MSc course in Introduction to Bioinformatics and Genomics, the data comes from NCBI but I gave it “easy” names for the students to work with it. Yesterday in the end they all used BUSCO 5.5.0 and it worked perfectly. The key problem is that I was not leaving selected MetaEuk as database, as I was working with prokaryotes, but I realized now that the code works with Prodigal in bacterial lineages even if there is no option to select it. I was then selecting Miniprot and I was getting the error. So to solve it it was only a matter of leaving MetaEuk selected for prokaryon genomes. Thanks for all the help! I am quite new in trying Galaxy, but this good support section is deffinitely a plus to recommend it to my colleagues that are not able to use the command line and would love to do bioinformatics! 🙂 ---
**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:** [January 17, 2025, 5:43pm UTC](https://help.galaxyproject.org/t/busco-fatal-error-exit-code-1/13544/6 "2025-01-17T17:43:47Z")