I am unsure how to interpret the .qzv output file from demux. Is the reverse read plot saying that I have few, if any reads? These are Mr DNA data. The raw reads were run through the FASTQ Processor available from Mr DNA to generate read 1, read 2, and index files. These files were then imported into QIIME2 and run through demux.
I was able to run these same data using QIIME1.9.
Thanks for your help.