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! 