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 0.4267574 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