Hello!
First of all, thank you for providing all the details and structuring your post. It saves a lot of time!
Based on your qzv files, your samples collected most of the issues that could decrease the number of output sequences:
- filtering (low scores)
- chimeras
- merging
Considering that you already removed the primers and discarded sequences without them, I can suggest:
- using 260 and 230 trunc. values for F and R reads
- decreasing minimum overlap to 6
- increasing max_ee values for F and R
- setting --p-min-fold-parent-over-abundance to, for example, 8 (not more than 16)
and see how it affects your stats.
Best,