Hi @thermokarst ,
I am getting the same error as @yipinto, but I’m pretty sure my barcodes are golay encoded. I am using the paired end EMP primers as described in Walters et. al: Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys, specifically the V4-V5 515f/926r primers . My understanding was that these are golay encoded. Here quoting from the table S1 description: "All Golay barcoded 515f/806r, 515f/926r, and ITS PCR primer and sequencing constructs. "
From the methods section “Modifications to PCR and sequencing primers”, they state: “We first modified the 515f/806r PCR primer construct by bar coding the forward primer, rather than the reverse primer, with 960 unique, 12-base Golay bar codes…” Is it possible that qiime is thrown off because the barcodes are on the forward instead of reverse primers? If so I would find that surprising though, because these primers are recommended by EMP (http://www.earthmicrobiome.org/protocols-and-standards/16s/).
Thanks for your help troubleshooting this new feature!