Just wanted to suggest developers to include some information in the help message for Dada2 regarding the number of output rep-seqs. Mainly that it can output fewer reads and that is not a feature-issue but more likely something related to failure in merging step etc.
I’ve had this question in the beggining and spent some time trying to understang plus people here have helped me finding out a solution. And it’s kind a everyday topic around.
I feel like this is a common issue for new users (like me) and people are going to be in panic after a faillure in Dada2 and, of course, will come here looking for hints to solve it. So, printing something like: “if Dada2 outputs few rep-seqs check the Qiime2 forum for the many related discussions” could point them to look for a solution that I believe they are going to easily find.