Hi @Marek_Koutny, to elaborate a bit on @colinbrislawn’s suggestion, what format are your reads in, and how did you import them? Please copy and paste your import command here. Also, what are the results when you run:
qiime tools peek single-end-demux.qza
That error message you posted means that the file single-end-demux.qza doesn’t contain SampleData[PairedEndSequencesWithQuality] or SampleData[SequencesWithQuality], which leaves @colinbrislawn’s suggestion that these data are SampleData[JoinedSequencesWithQuality]. If that is the case (and the peek command above will confirm that for us), that means you shouldn’t use DADA2, because that technique assumes that your paired-end reads aren’t pre-joined. You can look at using q2-deblur, check out this tutorial for more info. Thanks! 