Hi @Tania_Aires ,
Thanks for the update. If it is a big dataset (which sounds like it is), it very well may be worth your time to use the native R version of DADA2, following their recommended big data protocol. But also, that doesn't mean what you are running here is invalid, so if the data is complete that is totally fine as well!
Is this the FASTQ processor from Mr. DNA? If so, I just wanted to give a heads up that I have seen other folks with problems with Mr. DNA on this forum, especially that processor, for example a similar issue to yours here, and here, and several others if you just search Mr DNA on the forum. I personally have never used Mr. DNA but the easiest solution I can offer to avoid some headaches is to just use the raw FASTQ files without any processing. Unless there is something unique about the FASTQ processor that is required here.
FASTQ files without primers and barcodes etc. would be ideal but I understand they may charge extra for that. Removing those however is possible in QIIME 2 using various plugins too.