# Question about LEfSe input\_format.py when specifing no subclass
**URL:** https://forum.biobakery.org/t/question-about-lefse-input-format-py-when-specifing-no-subclass/253
**Category:** LEfSe
**Created:** [March 5, 2020, 8:12am UTC](https://forum.biobakery.org/t/question-about-lefse-input-format-py-when-specifing-no-subclass/253 "2020-03-05T08:12:40Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@darmecian](https://forum.biobakery.org/u/darmecian)
#### Post date: [March 5, 2020, 8:12am UTC](https://forum.biobakery.org/t/question-about-lefse-input-format-py-when-specifing-no-subclass/253/1 "2020-03-05T08:12:40Z")
Hello, I have a question to ask regarding the script input\_format.py, and subsequent run\_lefse.py.
I performed input\_format.py specifying no subclass (-s -1, meaning no subclass). However, when I examined output file, there are “subclass” row present in the table, which is the same name plus “\_subcl” as “class” (e.g. if class was “disease”, there was “disease\_subcl”). Is this behaviour okay?
If okay, when I run run\_lefse.py with the wilcoxon test option turned on, the script perform K-W and Wilcoxon for same grouping? I noticed that when I run with Wilcoxon test turned off, the script reported no p-value, while the p-value reported in the table are expected to be p-value from K-W test. so I ask whether it is okay to turn on the wilcoxon test when subclass are identical to class.
Thanks in advance.
**EDITED:**
I tried to attach files as minimum reproducible example using hmp\_small\_aerobiosis.txt in wikipedia of lefse, however, because of the limitation of new users, I could not.
the code is:
> format\_input.py hmp\_small\_aerobiosis\_sub.txt sample.in -f r -c 1 -u 2 -s -1 -o 1000000 --output\_table sample.input
> run\_lefse.py -r lda -l 2 -b 100 --wilc 0 --verbose 0 sample.in sample.res
input file is:
> hmp\_small\_aerobiosis\_sub.txt: raw input file, I removed the body\_site row from original file.
> sample.input: output file of format\_input.py, which have subclass row named “[class name]\_subcl”
> sample.res: output file of run\_lefse.py, which is without p-value
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### Author:  [@sma](https://forum.biobakery.org/u/sma)
#### Post date: [April 10, 2020, 7:06pm UTC](https://forum.biobakery.org/t/question-about-lefse-input-format-py-when-specifing-no-subclass/253/2 "2020-04-10T19:06:43Z")
Hi,
Many apologies for the long time to reply! If you didn’t find a solution, here’s a work-around to output p-values, while “not running” Wilcox filtering:
> [@P-values not calculated when wilc = 0](https://forum.biobakery.org/t/p-values-not-calculated-when-wilc-0/306):
>
> Hello, I have a dataset that is comparing multiple groups of samples and I previously had problems that the Wilcoxon test was being run even when I didn’t have subgroups. This forum helped me realize I needed to be using the --wilc 0 option to force it to not run the Wilcoxon test. My new problem arises in that now the p-values for the features passing the initial Kruskal-Wallis test are not being assigned a p-value. The output file is giving me a certain number of taxa that are passing the te…
Thanks!
Siyuan
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### Author:  [@darmecian](https://forum.biobakery.org/u/darmecian)
#### Post date: [April 22, 2020, 9:09am UTC](https://forum.biobakery.org/t/question-about-lefse-input-format-py-when-specifing-no-subclass/253/3 "2020-04-22T09:09:42Z")
Hello Siyuan,
Thank you very much for clarifying!