Error while trying to process data to LEfSe

Downstream analysis and statistics LEfSe
1

Hello, I am trying to analyze some metagenomic data using LEfSe, and I get the following error: Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 435, in
feats = numerical_values(feats,params[‘norm_v’])
File "/shed_tools/testtoolshed.

May I have your assistance please?
Thanks
Txt file Attached Sausages_genera.txt (115.1 KB)

2

Hi Elena,
If you look at the sample file we provide for Lefse (“73.txt”) you will see there are two identifier lines on the top, not three, so I removed one line.
Then there was something wrong with the headers, so I renamed the first line M1, M2… and the second ID1, ID2… and then it ran OK

3

Screen Shot 2020-11-06 at 7.31.05 AM
Screen Shot 2020-11-06 at 7.31.05 AM1436×866 176 KB
73.txt (82.9 KB)

4

Hi george-weingart,

Thank you so much for your help!