These are not beginner mistakes but I think that the AMF sequences are a little tricky so lets discuss some issues and steps forwards!
I personally would spend some time messing with parameters to get better % of sequences through. We would expect for their to be a smaller number of sequences since its low abundance but I would expect that you still get a higher percentage though the filter.
@SoilRotifer pointed out to me that the more your reads overlap the more chance there will be a mismatch, which will contribute to merge failures if the sequence hits the mismatch threshold. He recommends trimming 20-30 bases regardless of quality.
I would be point out that there is a chance that your AMF SSU region is too long to be covered by 2x300 seequnecing and in those cases there is nothing to do about the failure to merge.
I would mess around with truncating and see what that does for your % of sequence passed. I personally only like to mess with one parameter at a time. Once you have that sorted and have maximized the amount of sequences that are merge-able, I would look over this post to address your chimeric detection issue:
I hope this helps and let us know if you have any follow-up questions.
