Hi @H1889
I was just setting the default combinations at the top level to show what would be produced – my example isn’t a scientific example, more about the settings. I should have worded this better! I’ll try again.
You have bacterial data, correct? Using Metaeuk is the only requirement, the remainder you can set as needed. That can be “auto” for the linage as I used – but you can also choose a linage. In short, using Miniprot won’t work with the “auto” choice because it only functions with a linage selection.
Some more details are here. → https://help.galaxyproject.org/t/busco-for-bacterial-genome-assemblies/14475
Does this now help? 