# Busco tool keeps crashing **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** busco\ **Created:** [April 8, 2025, 6:54pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194 "2025-04-08T18:54:23Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 8, 2025, 6:54pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/1 "2025-04-08T18:54:23Z")
Hi there, I am trying to run BUSCO and it just keeps on crashing. Is there an issue with the tool? This started yesterday, I’ve been running BUSCO with no issues before then. Could you please look into this? Also, it does not give me an option to select lineage anymore, I don’t know whats going on. I am using [galaxy.eu](http://galaxy.eu) ---
**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:** [April 8, 2025, 9:23pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/2 "2025-04-08T21:23:33Z")
Hi @yamkela_mgwatyu The #busco tool form seems normal right now at [UseGalaxy.eu](http://UseGalaxy.eu). I am running some test runs in this history. - [https://usegalaxy.eu/u/jenj/h/test-busco](https://usegalaxy.eu/u/jenj/h/test-busco) If you want to share back your error as well we can troubleshoot all of the results. The form looks Ok to me so far but maybe I am missing what you have noticed. Thanks! 🙂 ---
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 10, 2025, 8:30am UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/3 "2025-04-10T08:30:04Z")
HI Jenna Thank you so much for contacting me back. it seems like busco still doesn’t work for me, I even tested it on datasets that worked before. I am getting this error > s | > > - desc: Fatal error: Exit code 1 () > - error\_level: 3 > - exit\_code: 1 > - type: exit\_code > > | > > - | - | > Job API ID | 11ac94870d0bb33a5a8a962929f18a4e | Job details are here [https://usegalaxy.eu/datasets/4838ba20a6d86765c770d749194c00b5/details](https://usegalaxy.eu/datasets/4838ba20a6d86765c770d749194c00b5/details) ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 10, 2025, 1:30pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/4 "2025-04-10T13:30:39Z")
Thanks for sharing the details of the job! The issue is that you’ve selected the _Eukaryota_ lineage database, but _All taxonomic groups_ in the autodetect lineage section. With this combination, busco will look for lineage files from all phyla in the DB, including archaea, prokaryotes, etc., which it then fails to find in that _Eukaryota_-only DB, hence the error. You can combine: - the _Eukaryota_ DB with _“auto-lineage group”_: _Eukaryotes_, or - the _Lineage datasets all_ DB with _“auto-lineage group”_: “All taxonomic groups” and both should result in a successful tool run. Arguably, the tool should make this requirement clear because you are not the first user falling into this trap. ---
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 10, 2025, 1:59pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/5 "2025-04-10T13:59:35Z")
Hi there, But it doesn’t even give me an option to select lineage, because normally I’d select “fabales” > **(attachments)** > > ![Screenshot 2025-04-09 at 13.00.17.png](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/e3a42a927ded1ba9c1d8d0492cd4dae3fbab8088.png) ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 10, 2025, 2:45pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/6 "2025-04-10T14:45:47Z")
don’t go for that “Select lineage” option, but for “Auto-detect”. Then in the next select menu choose “Eukaryotes”. ---
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 12, 2025, 5:45pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/7 "2025-04-12T17:45:19Z")
That is what I’m doing and it still doesn’t work. ---
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 13, 2025, 2:09pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/8 "2025-04-13T14:09:12Z")
```auto 2025-04-12 21:27:40 ERROR: Unable to run BUSCO in offline mode. Dataset /data/db/data_managers/busco/eukaryota+2024-03-23-082359/lineages/fabales_odb10 does not exist. 2025-04-12 21:27:40 ERROR: BUSCO analysis failed! 2025-04-12 21:27:40 ERROR: Check the logs, read the user guide ([https://busco.ezlab.org/busco_userguide.html](https://busco.ezlab.org/busco_userguide.html)), and check the BUSCO issue board on [https://gitlab.com/ezlab/busco/issues](https://gitlab.com/ezlab/busco/issues) ``` I am getting this error. It seems like the other databases have not been installed. ---
**Author:** ![yamkela\_mgwatyu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/yamkela_mgwatyu/32/4205_2.png) [@yamkela\_mgwatyu](https://help.galaxyproject.org/u/yamkela_mgwatyu)\ **Post date:** [April 14, 2025, 6:59pm UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/9 "2025-04-14T18:59:33Z")
Hi there, Did you get a chance to look into this? ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 15, 2025, 11:33am UTC](https://help.galaxyproject.org/t/busco-tool-keeps-crashing/15194/10 "2025-04-15T11:33:38Z")
Partially. So, turns out that `Eukaryota (2024-03-23)` doesn’t contain _all_ eukaroyte lineages and specifically not `Fabales`, which matches your data. The correct way to make things work is to: 1. Select `Busco v5 Linage Datasets (all+2024-03-21)` as the Cached database 2. Restrict lineage consideration to just Eukaryotes with _“auto-lineage group”_: `Eukaryotes` With that, busco will run succesfully and produce stats for _Fabales_. However, I’ve encountered an additional issue then, for which I don’t have a solution atm and which will likely require a tool update: the _short summary_ and the _full table_ dataset outputs of busco will both be empty and you will have to rely on the tool’s standard output (one of the sections on the dataset details page). As long as you do not intend to use the datasets in downstream steps that would be ok, but it’s far from ideal of course. Some of the optional additional outputs of the tool _will_ get generated correctly, but I cannot tell you exactly which atm so maybe try to enable everything and use what works and makes sense to you.