make.shared seq not in group file

mothur bugs
#1

I’m trying to make a shared file and keep running into this

[ERROR]: F4Q4SKU06G006T is in your listfile and not in your groupfile. Please correct. (150,000 times)

But when I use grep to search for a few of the missing sequences in the group file, I find them. This is a huge dataset with sequences from many runs so it’s completely possible that I inadvertently introduced a weird character when concatenating, but I haven’t been able to find it. Ideas on where to start looking?

#2

Alright if anyone else comes across this, it was user error (shocking, I know). When making my concatenated fasta/names files I duplicated one plate. So the sequences were in the group file once but in the fasta and names file twice.