Welcome @sophiaescobar !!
I just checked the data at UseGalaxy.org and everything was working as expected. The UseGalaxy.org.au server should be using this same data through a shared CVMFS repository.
Shared history: https://usegalaxy.org/u/jen-galaxyproject/h/test-busco-2025-01
Screenshot of some of the test jobs with parameters tagged (you can explore the shared history for exact details).
Important keys: please notice how the Select a gene predictor must be set to metaeuk to allow the selection of the bacterial lineage. All prokaryotic lineages will require this same gene predictor.
For eukaryotic, you can use either of the predictors.
[1]
This is a good question so I’m glad you asked again, and I understand your point about suspecting that the gene predictor setting is unexpectedly specific!
But this is known and intentional for now – at the UseGalaxy public servers, the computed indexes for prokaryotic genomes are only available for use with the metaeuk option. This leads to Prodigal being used (technically!). Bacterial lineage index for miniprot are not available at this time.
[2]
The tool is a bit complicated with all of the options and the comprehensive indexes! Hopefully this explains what is going on.. but does this actually help?
Screenshot from the shared history, with the history panel’s datasets displayed, and the rerun form for dataset 14 shown. ↩︎
Screenshot from the Busco 5.8.0+galaxy1 tool form showing option Select a gene predictor. Tool tip: In the case of a prokaryotic genome, Prodigal is the default gene predictor. ↩︎