I am using Prokka and Roary in https://usegalaxy.eu/ . There are several errors in the execution of the pipeline.
-Prokka does not output results in .gff3 format, depite the fact that there is an option in Prokka parameters for gff version 3 output.
-Roary will not work with the output of Prokka and will output an error.
-When renaming the .gff files to .gff3 extention, Roary runs successfully, however with default settings, it rarely finds core genes, and all of the genes identified shift to cloud or shell genes.
-I tried with the data from a published study (https://www.liebertpub.com/doi/abs/10.1089/omi.2019.0005?rfr_dat=cr_pub%3Dpubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&journalCode=omi) and cannot reproduce the results, even though I run the same parameters that the authors describe.
Please adress this issue.