I am using MiSeq SOP and running on Widows. I have not used mothur for several months and seem to have forgotten how to format the stability.files input. When I go to make contigs mother is only seeing the first set of read 1 and read 2 files, and then saying it can not find the rest. then generates contigs for the first sample only. I didn’t have this problem before, so obviously I forgot something, or did something correctly by chance previously.
Here’s a link to the format mothur expects in the file, http://www.mothur.org/wiki/Make.contigs#file.