miseq SOP unique.seqs in your fasta file, sequence names must be unique, please correct.

Hi,

I am working through my first batch of miseq data (have successfully ran several 454 projects). I am early on in the pipeline. Ran the make.contigs, summary and screen.seqs. My issue comes in at the unique.seqs command. I get thousands of these error and I am not sure how to go about fixing it.

**************************** is in your fasta file, sequence names must be unique, please correct.

The command finishes without crashing but the next command, count.seqs, sends up even more red flags (errors).

Any ideas?

Patrick

Could you post the commands you ran?