Hi @jwdebelius,
I have relaxed the dada2 parameters of trimming (setting --p-trim-left -f/-r and --p-trunc-len-f/-r to 0) and it works! After that the alignment step run!! (I made a comparation between the kmer db file and the rep-seqs dada2 file and find than the seqs did not start on the same position, so that was the error I was not awared of)...
However, I think I still need to adjust dada2... I am not feel confident with this step.
Yes, I think that is a good idea. Maybe an error message as "alignment file hasn't show any matches" or something similar?
Also, I was wondering about this: q2-sidle running out of memory at reconstruct-counts.
In this moment I am executing the reconstruction step (finally!! 
) and (even though I set the --p-cores parameter to 8) it only uses one core. Maybe there is an estimation of the running time? It has been running for at least 8 hours instead.
Again, thank you so much for kindness and for responding so quickly!!
Best,
Elsa