Welcome, @Zbourhane
This is your question at the other forum, yes? Keep following up where you are right now at → LEfSe issues and errors - #38 by Zee - LEfSe - The bioBakery help forum
The problems with this tool seem to be server side, and those scientists are the only people who can fix it. They want people to use the updated pipeline for both scientific and technical reasons – read about that in their other topics.
For everyone who has a problem at the Biobakery Galaxy server, we have this message to share. We would like to help but can’t in any practical way due to the unique nature of that server’s “wrapped tools” and how the server is hosted.
So, since those wrapped tools are unique and different from the other public Galaxy servers, you could also explore the alternative Lefse tools as part of the Mothur pipeline at one of the UseGalaxy servers. It works a bit differently but maybe interesting anyway – and the original tool publication would apply. Search the tool panel with the tool name to find it. Search the GTN tutorials and workflows for how to prepare the data for that kind of pipeline (keyword “mothur”). Lefse isn’t covered specifically but the tutorials will help to get your data organized and ready.
Hope this helps!
Prior Q&A here → How to fix errors with Lefse - #4 by jennaj