I had the same issue when using the online tool of LEfSe and I could not choose the class option as well.
In my case, I prepared the txt file from qiime2 output to LEfSe format text file in LibreOffice and then
tried to solve this problem with Python 2.7, but I got the error message as below.
“if r in [‘0’,‘1’,‘2’,‘3’,‘4’,‘5’,‘6’,‘7’,‘8’,‘9’,’_’]: indexerror: string index out of range”
So, I made the tab delimited text file (.tsv) with the other program, Excel in MS Office.
Surprisingly, the file did work well in both online LEfSe and python 2.7, and the class and subclass were identified in LEfSe system.
I did not find the differences between the txt file from LibreOffice and from Excel, but I think if you change some values (ex, round up) or prepare the new text file again in a different way, you could analyze your data like my case.
Hope you can solve this problem.
with Best regards,