Yes, your log messages are expected when attempting to combine Miniprot and an archaea lineage. Instead, toggle the first option back to the default to use MetaEuk.
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.
How the indexes are organized is a bit complicated! Any server that uses the base public Galaxy pre-computed indexes will work this way, and that includes all UseGalaxy servers. Setting the form up this way routes the jobs to the clusters that can process the request (the tool, dependencies, and index data combinations). Please give this a try and let us know if it works for you!
