No summary output after lefse

Hi, this is my first time using mothur in R (following the video by Dr. Schloss). I successfully ran lefse for 5 of my dataset and get the output summary. However, I did not get any output from running lefse of my 6th dataset. There is only one number in the output which I’m not sure if it is related to my data size or it’s a specific code for a message behind?

mothur > lefse(shared=asv3_ca.shared,, inputdir=LDA_data)
Setting input directories to:

[1] 884

How many treatment groups are in It would be good to visually count the number of replicates of each group in that desgin file.


Hi Dr. Schloss, thank you very much for the reply!

I have 2 groups in, one group has 9 people, the other has 48 people. My data is a longitudinal data, so I seperate them by time point. In my previous lefse analyses I used the same data (same participants) as my, and they went well. I’m wondering if no summary output is due to no significant feature found between groups? Thank you!