Did you finally find the solution? I’ve got the same problem as well. I run roary for 37 e coli genomes, but the core genome alignment file is empty and there is no sequences come out
All of the UseGalaxy.* servers have been updated to the latest tool version:
Galaxy Version 3.13.0+galaxy2. If this is not the version you are running, please try with the updated wrapper.
I updated the ticket with the details about the resolution addressing the “spaces in names” issue.
I’m going to split off your question into a new topic. If you want more help, would you please post back a shared history link? Sharing your History You can also start up a rerun in that same history if you haven’t already (reruns resolve transient failure reasons).
Test history with example usage: https://usegalaxy.org/u/jen/h/test-prokka-roary