12423828 total bases in 49536 reads from 5 samples will be used for learning the error rates.
12415082 total bases in 49536 reads from 5 samples will be used for learning the error rates.
Sample 1 - 9909 reads in 5696 unique sequences.
Sample 2 - 9932 reads in 5914 unique sequences.
Sample 3 - 9983 reads in 9769 unique sequences.
Sample 4 - 9819 reads in 5762 unique sequences.
Sample 5 - 9893 reads in 5506 unique sequences.
Sample 1 - 9909 reads in 9828 unique sequences.
Sample 2 - 9932 reads in 9902 unique sequences.
Sample 3 - 9983 reads in 9976 unique sequences.
Sample 4 - 9819 reads in 9736 unique sequences.
Sample 5 - 9893 reads in 9852 unique sequences.
null device 
          1 
Run 0 stress 0 
Run 1 stress 0 
... Procrustes: rmse 0.3838412  max resid 0.4989586 
Run 2 stress 0 
... Procrustes: rmse 0.3639025  max resid 0.5433757 
Run 3 stress 0 
... Procrustes: rmse 0.3025473  max resid 0.3854776 
Run 4 stress 0 
... Procrustes: rmse 0.2584814  max resid 0.4686797 
Run 5 stress 0 
... Procrustes: rmse 0.3623849  max resid 0.4941675 
Run 6 stress 0 
... Procrustes: rmse 0.3070594  max resid 0.472967 
Run 7 stress 0 
... Procrustes: rmse 0.3440168  max resid 0.4811764 
Run 8 stress 0 
... Procrustes: rmse 0.4155433  max resid 0.5513238 
Run 9 stress 0 
... Procrustes: rmse 0.3169249  max resid 0.5676811 
Run 10 stress 0 
... Procrustes: rmse 0.3710072  max resid 0.4978922 
Run 11 stress 0 
... Procrustes: rmse 0.39001  max resid 0.513511 
Run 12 stress 0 
... Procrustes: rmse 0.3259815  max resid 0.4592674 
Run 13 stress 0 
... Procrustes: rmse 0.4085605  max resid 0.5791099 
Run 14 stress 0 
... Procrustes: rmse 0.385942  max resid 0.5751405 
Run 15 stress 0 
... Procrustes: rmse 0.3041421  max resid 0.5016141 
Run 16 stress 0 
... Procrustes: rmse 0.4321483  max resid 0.5863752 
Run 17 stress 0 
... Procrustes: rmse 0.2558686  max resid 0.3195557 
Run 18 stress 0 
... Procrustes: rmse 0.2059728  max resid 0.2979681 
Run 19 stress 0 
... Procrustes: rmse 0.296693  max resid 0.4288962 
Run 20 stress 0 
... Procrustes: rmse 0.2788784  max resid 0.4049208 
*** No convergence -- monoMDS stopping criteria:
    20: stress < smin
null device 
          1 
null device 
          1 

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