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 0.3838412 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