Busco tool keeps crashing

usegalaxy.eu support
1

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

2

Hi @yamkela_mgwatyu

The busco tool form seems normal right now at UseGalaxy.eu.

I am running some test runs in this history.

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! :slight_smile:

3

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

4

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.

5

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
Screenshot 2025-04-09 at 13.00.17.png2880×1800 727 KB

6

don’t go for that “Select lineage” option, but for “Auto-detect”.
Then in the next select menu choose “Eukaryotes”.

1 Like
7

That is what I’m doing and it still doesn’t work.

8 
           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.

9

Hi there,

Did you get a chance to look into this?

10

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.