ValueError: could not convert string to float: "whole"? #16

Downstream analysis and statistics LEfSe
1

hello could you please let me know why I am getting this error when I try to convert my data file into lefse input?
$ lefse_format_input.py lefseGalaxy.txt lefseGalaxy.in -c 1 -s 2 -u 3 -o 1000000

image
image725×277 109 KB

attached the file
lefseGalaxy.txt (429.3 KB)

2

It looks to me like you have several variables in the dataset that aren’t used in the LEfSe call, which can create problems. If you remove the extra variables and only keep the class, subclass (if applicable), and ID variable (if applicable) in addition to your read data, that may fix the problem.
Best,
Meg

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