Results generated by running the recipe.
Parameters used during the run:
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
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