Hi @fvalbores!
Excellent!
Are you attempting to use your quality-filtereded sequences now? If you are still using your filenames from above, it looks like you aren't - just wanted to double check with you what your intentions are (paired-end-demux.qza vs demux-filtered.qza.
DADA2
Generally speaking, we don't recommend quality-filtering reads prior to processing in DADA2, because DADA2 performs error correction prior to filtering reads. If you want to use DADA2, I would use your imported sequences (paired-end-demux.qza) and run those right into q2-dada2. If you did that, please let me know (see my note above about your filenames).
deblur
If you were accidentally using your unfiltered sequences with q2-deblur (see my note above about filenames), that is likely the problem, and you just need to update your command to use the correct artifact. If the filenames are in fact correct, and you are using your quality filtered sequences as input to q2-deblur, I would suggest running demux summarize on the filtered sequences, and sharing that here.
Thanks! 