I got a sequencing data from a commercial laboratory with very power sequencing quality. It was not possible to process them for DADA2 using paired end protocol. See the attachment od DADA2.
Then I used only forwarded reads and aligned them against gg-13-8-99-515-806-nb-classifier.qza
At then end of the day I got only 99% taxonomy upto Kingdom level. See attachment.
Shall I try something other to get at least some phylogeny information? May be I used incorrect gg reference or the result is because of poor sequencing quality?