Hey @Dean - I suspect something is quite right with your barcodes. Can you provide the following:
- What version of QIIME 2 are you running?
- Can you confirm that your reads are single-end? I see you are running
dada2 denoise-single, but want to be sure.
I was going to ask you to run head on all of your files (before and after extracting barcodes in Q1), but, I realized this might be a great use case for q2-cutadapt! You should be able to skip Q1 here, and just import your raw (barcoded) reads, then use the cutadapt demux-single command to demultiplex these reads. How about you give that a shot (check out the Community Tutorial for some assistance, too)? That might be easier, and we can’t really provide support for Q1 anymore, which is likely where the issue you originally reported is cropping up. Keep us posted! 