Hi @11112 ,
Are you comparing running q2-dada2 under identical settings on 2 different machines? Or as @colinbrislawn was hinting at comparing q2-dada to stand-alone DADA2 in R?
Can you also let us know what these 'differences' are exactly with some more detail?
One thing that may be happening, though I'd have to check how QIIME 2 handles this under the hood, is that if you transferring your files to other systems, and during the transfer the order of your samples are changing? Say in one run you import your data as S1, S2, S3, and in other S3, S2, S1, then the first 1,000,000 reads in --p-n-reads-learn, that is drawn by DADA2 for its training model, may reflect different reads. But still, even with all that I wouldn't expect drastic differences, so I am interested to hear some more more details on this.