DADA2 Classification
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Run Parameters
Parameters used during the run:
  • 16S Reference Database.: SILVA
  • Minimum read length: 100
  • Taxonomical rank to report: Phylum

Result description.

Output Messages
Messages printed to the standard output stream:
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 0.3887969  max resid 0.6132114 
Run 2 stress 0 
... Procrustes: rmse 0.4243603  max resid 0.5962747 
Run 3 stress 0 
... Procrustes: rmse 0.2295172  max resid 0.3702913 
Run 4 stress 0 
... Procrustes: rmse 0.3825837  max resid 0.5911347 
Run 5 stress 0 
... Procrustes: rmse 0.3777222  max resid 0.6582638 
Run 6 stress 0 
... Procrustes: rmse 0.3988615  max resid 0.5445545 
Run 7 stress 0 
... Procrustes: rmse 0.4023602  max resid 0.5312996 
Run 8 stress 0 
... Procrustes: rmse 0.3297325  max resid 0.3902133 
Run 9 stress 0 
... Procrustes: rmse 0.2549185  max resid 0.309095 
Run 10 stress 0 
... Procrustes: rmse 0.3606613  max resid 0.4863845 
Run 11 stress 0 
... Procrustes: rmse 0.3626546  max resid 0.480152 
Run 12 stress 0 
... Procrustes: rmse 0.3789594  max resid 0.6396095 
Run 13 stress 0 
... Procrustes: rmse 0.2110531  max resid 0.3399797 
Run 14 stress 0 
... Procrustes: rmse 0.3391285  max resid 0.4330274 
Run 15 stress 0 
... Procrustes: rmse 0.2914256  max resid 0.3614437 
Run 16 stress 0 
... Procrustes: rmse 0.3905838  max resid 0.5583127 
Run 17 stress 0 
... Procrustes: rmse 0.3816237  max resid 0.5633881 
Run 18 stress 0 
... Procrustes: rmse 0.3895844  max resid 0.5701147 
Run 19 stress 0 
... Procrustes: rmse 0.2186731  max resid 0.3709631 
Run 20 stress 0 
... Procrustes: rmse 0.4352569  max resid 0.6038356 
*** No convergence -- monoMDS stopping criteria:
    20: stress < smin
null device 
          1 
null device 
          1 
Other Messages
Messages printed to the standard error stream:
Loading required package: dada2
Loading required package: Rcpp
Loading required package: phyloseq
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

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