Hello there,
This seems very similar to this question that was asked recently, though I’m not sure if my suggestion worked for that asker. I am curious where you’re seeing the following command, as I did not see it when I followed the link to the tutorial you sent: lefse-format_input.py hmp_small_aerobiosis.xls hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
When I follow the link you sent, I see documentation that gives the following command:
format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
The version I am using is the biobakery (not bioconda) version of LEfSe, which I installed using the following command:
conda install -c biobakery lefse
The version I have is 1.0. Perhaps try re-installing with the above command, and if that doesn’t work, please let me know!
Thanks,
Meg