Hi @MiriamGorostidi,
I probably would have trimmed the forward adapter, but it looks like this is mostly working.
Please check your sequence quality and trim length, because that's where you're losing data (likely due to a quality drop at the end). There are a lot of posts on the forum about how to judge dada2 quality; it might be good to look at those to better understand how to use your dada2 summary to guide trimming.
Best,
Justine