Hi @EliCas1
Are you working at this server? If so, the older Lefse tools had some trouble earlier and as far as I know, have been replaced with a new workflow pipeline. This is clarified at the forum the Biobakery team hosts.
If you click on that tag you can see the prior conversations, and the forum itself has a few threads where the developers and scientists report the current status.
Hope this helps and if I guessed wrong about where you are working, we can follow up more. The server URL would be helpful to get started (find this at the very top of your browser window).
Thanks! 