Loading required package: dada2
Loading required package: Rcpp
Loading required package: phyloseq
Creating output directory: ./filtered
1186 paired-reads (in 11 unique pairings) successfully merged out of 6784 (in 257 pairings) input.
1640 paired-reads (in 18 unique pairings) successfully merged out of 5124 (in 144 pairings) input.
880 paired-reads (in 3 unique pairings) successfully merged out of 1643 (in 30 pairings) input.
2623 paired-reads (in 27 unique pairings) successfully merged out of 6214 (in 299 pairings) input.
3574 paired-reads (in 36 unique pairings) successfully merged out of 6011 (in 169 pairings) input.
Warning message:
In estimate_richness(physeq, split = TRUE, measures = measures) :
  The data you have provided does not have
any singletons. This is highly suspicious. Results of richness
estimates (for example) are probably unreliable, or wrong, if you have already
trimmed low-abundance taxa from the data.

We recommended that you find the un-trimmed data and retry.
Warning messages:
1: In metaMDS(veganifyOTU(physeq), distance, ...) :
  stress is (nearly) zero: you may have insufficient data
2: In postMDS(out$points, dis, plot = max(0, plot - 1), ...) :
  skipping half-change scaling: too few points below threshold