Using Sff.multiple

Newbie alert:

I’ve used sff.multiple to combine several (11 ) .sff files, but when I try to pick up the Schloss SOP at the unique seq step with the file that I am pretty sure combines them all (named sfffiles.sffffiles.fasta in my case, I had named the file which lists the .sff files to work on sfffiles.txt) the number of unique sequences only changes by 300 (to total some 13,500ish sequences). What can I be doing wrong? Some ofthese samples are replicates, so presumably should share sequences.


If you send your input files and logfile to, I will take a look.