LEfSe - What are the parameters at the end of lefse_format_input.py

Downstream analysis and statistics LEfSe
1

I’m running into issues when using LEfSe on a dataset containing multiple groups within the sample.

In this case there are 5 groups and I’m getting the error ValueError: could not convert string to float: 'only'

When I run the analysis on only 2 of the groups it run’s fine, producing the LDA scores and Cladogram.

I’m wondering if that has anything to do with the parameters at the end of the format command in the tutorial:

$ lefse_format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000

Specifically: -c 1 -s 2 -u 3 -o 1000000

Can anyone tell when what these represent and if it has any relevance to the number of groupings in the sample?

Failing that, is there any explanation why I can’t run the analysis on a sample with 5 groups?

2

The first thing I’d check is that the order of your variables is correct. As a reminder, -c 1 means that the first row is the class variable, -s 2 means the second row is the subclass variable, and -u 3 means the third row is the subject ID. If there is no subject ID variable, don’t have any -u option in your call to lefse_forma_input.py, and likewise, if there’s no subclass variable, don’t have any -s option in your code.
Let me know if that helps!
Best,
Meg