I encountered the same problem as the user GillSie Sierra G ( Demux EMPPaired Error without rev-comp-mapping-barcode - User Support - QIIME 2 Forum), and I read and implemented his solution, but it didn't work for me.
So, I have to create a new post to ask for help.
For studying Qiime2, I have forward.fastq.gz, reverse.fastq.gz, barcodes.fastq.gz and mapping_file.tsv downloaded from Qiita (ID 11635). I think it matches the type EMP-paired and it looks like that there are no barocdes and primers in forward.fastq.gz and reverse.fastq.gz.
Here are my operation steps and error reporting
Step1: I have imported my files as EMP-paired using the command:
qiime tools import
Step2: I used the following code to demultiplex and got the "demux03.qza" successfully.
qiime demux emp-paired
qiime demux summarize
However, when viewing "demux-full.qzv", the sequence counts dropped dramatically after the first two samples and looked so strange.
I have try the code "--p-no-golay-error-correction" and "--p-rev-comp-barcodes" to replace and I failed (I put my attempts and errors below).
What did I do wrong? What should I do?
Any suggestion will help me , and I will be very grateful !!