Group File looses group identifier

I am processing 454 GsJr data, this is my first time working with my own data, but have worked through the SOPs without any issues. I have 11 samples identified with my oligos file. After I perform shhh.flows I am outputted with a ID.shhh.names, ID.shhh.count, ID.shhh.fasta, and ID.shhh.qual file for each sample (represented by ID) and a .shhh.fasta and .shhh.names for the combined sff file. I merged all of the group files to get a combined group file. At some point in my analysis (not sure where) my group file gets changed and all of the sample ID’s in the group file change to "y"s witha hat and I can no longer differentiate where my samples came from? Any ideas?

Hmmm, not sure what’s going on - but…if you’re following the SOP, you shouldn’t need to merge group files - you’d generate group files when you run trim.seqs after shhh.flows. Give that a shot and see if things improve.