I was following Mealybug’s mothur pipeline analysis guidelines on a different dataset and everything was fine until “Clustering sequences in OTUs” step. In this, when I am running the “make.shared” command, I am not getting the rabund files for the 42 samples I have, as should be formed. Only the .shared file is generated.
What could be the possible mistake that I might have made?
Also, if it is of any help - I don’t have any mock community for assessing the error rates in my sample.