BUSCO Fatal error: Exit code 1 ()

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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:

|            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
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. :disappointed_relieved:

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Welcome, @mmontonerin :slight_smile:

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 works. I’ll be testing that too but maybe gets you a quicker “fix”.

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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

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. 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. :slight_smile:

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This was very helpful! Changing to version 5.5.0 worked perfectly :slight_smile:

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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! :slightly_smiling_face:

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