Hello,
I ran through the tutorial and it works as intended for me (the grouping variable is correct), and I wanted to check that you’re using the latest version of lefse and the tutorial. Here is the link to the tutorial I was following:
I ask because the commands you pasted above are slightly different from the ones used in the tutorial ("lefse-format_input.py vs format_input.py, for instance).
Could you try running “conda update lefse” and then re-following the tutorial linked above, and letting me know if it works?
Thanks,
Meg