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 0.4267574  max resid 0.5994115 
Run 2 stress 0 
... Procrustes: rmse 0.2968956  max resid 0.3890192 
Run 3 stress 0 
... Procrustes: rmse 0.2542193  max resid 0.3848344 
Run 4 stress 0 
... Procrustes: rmse 0.3629642  max resid 0.4599566 
Run 5 stress 0 
... Procrustes: rmse 0.2891944  max resid 0.4350951 
Run 6 stress 0 
... Procrustes: rmse 0.3770757  max resid 0.4854623 
Run 7 stress 0 
... Procrustes: rmse 0.3614451  max resid 0.5147593 
Run 8 stress 0 
... Procrustes: rmse 0.3540697  max resid 0.4525209 
Run 9 stress 0 
... Procrustes: rmse 0.3548343  max resid 0.5856491 
Run 10 stress 0 
... Procrustes: rmse 0.3710783  max resid 0.6035313 
Run 11 stress 0 
... Procrustes: rmse 0.3295353  max resid 0.3705275 
Run 12 stress 0 
... Procrustes: rmse 0.4044058  max resid 0.5721898 
Run 13 stress 0 
... Procrustes: rmse 0.4276179  max resid 0.6076075 
Run 14 stress 0 
... Procrustes: rmse 0.3793138  max resid 0.4834029 
Run 15 stress 0 
... Procrustes: rmse 0.3661588  max resid 0.5179157 
Run 16 stress 0 
... Procrustes: rmse 0.3335926  max resid 0.483971 
Run 17 stress 0 
... Procrustes: rmse 0.2796336  max resid 0.3939244 
Run 18 stress 0 
... Procrustes: rmse 0.3629375  max resid 0.4985937 
Run 19 stress 0 
... Procrustes: rmse 0.4214195  max resid 0.5878209 
Run 20 stress 0 
... Procrustes: rmse 0.3593711  max resid 0.637448 
*** 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