Improved export for volcano plot, debug diversity confidence interval

Dockerfile

@@ -38,10 +38,10 @@ RUN wget --no-verbose https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz -P
     wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
     gdebi -n ss-latest.deb && \
     rm -f version.txt ss-latest.deb && \
-    wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201909.tar.gz -P /opt && \
+    wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202007.tar.gz -P /opt && \
     mkdir /opt/packman
 
-RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_201909.tar.gz', '/opt/packman')"""
+RUN R -e """install.packages('packrat', repos='http://cran.univ-paris1.fr/');library("packrat");packrat::unbundle('/opt/shaman_package_202007.tar.gz', '/opt/packman')"""
 
 COPY docker_inst/shiny-server.conf  /etc/shiny-server/shiny-server.conf
 COPY docker_inst/.Rprofile  /srv/shiny-server/

README.md

@@ -50,13 +50,13 @@ chmod +x ./shaman/www/shaman.R && Rscript ./shaman/www/shaman.R
 SHAMAN is available for R=3.6.1. Packrat framework allows an easy installation of all the dependencies. Of note, raw data submission is not possible with this version.
 ```
 # Download packrat package
-wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_201908.tar.gz
+wget ftp://shiny01.hosting.pasteur.fr/pub/shaman_package_202007.tar.gz
 mkdir packrat/shaman
 ```
 Now you can run R:
 ```
 install.packages("packrat")
-packrat::unbundle("shaman_package_201908.tar.gz", "packrat/shaman")
+packrat::unbundle("shaman_package_202007.tar.gz", "packrat/shaman")
 packrat::init("packrat/shaman")
 system("Rscript -e 'shiny::runGitHub("pierreLec/KronaRShy",port=5438)'",wait=FALSE),
 shiny::runGitHub('aghozlane/shaman')

Rfunctions/TablesPlot.R

@@ -209,7 +209,7 @@ Volcano_Plot <- function(input, data, export = FALSE) {
                          axis.text = element_text(size = input$axisFontSize),
                          legend.title = element_text(size = input$axisFontSize),
                          legend.text = element_text(size = input$axisFontSize))
-    plot <- plot + geom_text(aes(label = labels, color = color_var), size = input$labelsSize %/% 3, hjust = 1, vjust = 1, show.legend = FALSE)
+    plot <- plot + geom_text_repel(aes(label = labels, color = color_var), size = input$labelsSize %/% 3, hjust = 1, vjust = 1, show.legend = FALSE)
     plot <- plot + scale_color_manual(name = "Group", values = c("Down" = input$colour1,"Not significant" = input$colour2,"Up" = input$colour3))
     if(input$showSignifThresholds){
       plot <- plot + geom_hline(yintercept = y_signif, linetype = "dashed", size = input$signifThresholdsWidth/2)

Rfunctions/VisuPlot.R

@@ -450,32 +450,32 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE, alpha_transparen
     alpha=alpha[alpha_selected]
     alpha_sd = tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, sd)
     alpha_sd=alpha_sd[alpha_selected]
-    ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb[alpha_selected],0)
-    ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb[alpha_selected]
-    
+    ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb,0)
+    ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb
+
     shan <- tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, mean)
     shan_selected = !is.na(shan)
     shan = shan[shan_selected]
     shan_sd = tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, sd)
     shan_sd = shan_sd[shan_selected]
-    ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb[shan_selected],0)
-    ci.shan.up = shan + 1.96*shan_sd/sqrt.nb[shan_selected]
+    ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb,0)
+    ci.shan.up = shan + 1.96*shan_sd/sqrt.nb
     
     simpson <- tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, mean)
     simpson_selected = !is.na(simpson)
     simpson = simpson[simpson_selected]
     simpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, sd)
     simpson_sd = simpson_sd[simpson_selected]
-    ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb[simpson_selected],0)
-    ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb[simpson_selected]
+    ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb,0)
+    ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb
     
     invsimpson <- tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, mean)
     invsimpson_selected = !is.na(invsimpson)
     invsimpson = invsimpson[invsimpson_selected]
     invsimpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, sd)
     invsimpson_sd = invsimpson_sd[invsimpson_selected]
-    ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected],0)
-    ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected]
+    ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb,0)
+    ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb
     
     gamma <- TaxoNumber(counts_tmp_combined, targetInt$AllVar)
     gamma = gamma[!is.na(gamma)]

www/masque/done/filea1a9748bebd0.json

+{"type": "16S", "path_R2": "/tmp/Rtmp6ySBtN/Masque_files_R2", "phredthres": 0, "annotationstrand": "both", "aFmax": 0.945, "aPmin": 0.75, "aSmin": 0.98, "aKmin": 0.75, "minreadlength": 50, "mail": "amine.ghozlane@pasteur.fr", "clusteringthreshold": 0.97, "aOmax": 0.865, "contaminant": "/tmp/Rtmp6ySBtN/filea1a9748bebd0_contaminant.fasta", "name": "filea1a9748bebd0", "pattern_R1": "_L001_R1_001", "clusteringstrand": "both", "aCmin": 0.785, "minampliconlength": 50, "aPmax": 0.785, "dreptype": "--derep_prefix", "maxampliconlength": 0, "data_history_name": "data_shaman_2186_106", "minoverlap": 10, "aOmin": 0.82, "aGmin": 0.945, "path_R1": "/tmp/Rtmp6ySBtN/Masque_files_R1", "aFmin": 0.865, "paired": true, "result_history_name": "shaman_2186_106", "mincorrect": 50, "minabundance": 4, "host": "", "aGmax": 0.98, "aCmax": 0.82}
\ No newline at end of file

www/masque/done/filea1a9748bebd0/shaman_greengenes_annotation.tsv

+OTU	Kingdom	Phylum	Class	Order	Family	Genus	Specie
+OTU_15	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+OTU_45	Bacteria	Cyanobacteria	4C0d-2	MLE1-12			
+OTU_14	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae		
+OTU_4	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_20	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae		
+OTU_19	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_25	Bacteria	Firmicutes					
+OTU_1	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_42	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_70	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_59	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae		
+OTU_60	Bacteria	Firmicutes	Bacilli	Gemellales			
+OTU_67	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_46	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae		
+OTU_65	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Sneathia	
+OTU_44	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	S24-7		
+OTU_18	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	
+OTU_49	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_66	Bacteria	Firmicutes	Bacilli	Lactobacillales			
+OTU_40	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+OTU_38	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_2	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	aureus
+OTU_11	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae		
+OTU_24	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium	acnes
+OTU_6	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_5	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	enterica
+OTU_69	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_43	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_53	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_3	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+OTU_47	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+OTU_8	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
+OTU_61	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_9	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_12	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_55	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_62	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_26	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
+OTU_28	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_7	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_52	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	

www/masque/done/filea1a9748bebd0/shaman_greengenes_tree.nhx

+(OTU_43:0.042884653,(OTU_4:0.000000007,OTU_46:0.009390584)0.912:0.017870958,(OTU_49:0.020821676,(OTU_47:0.022300505,((((OTU_66:0.000000007,(OTU_61:0.045356270,((OTU_69:0.000000007,OTU_60:0.039062501)0.731:0.000000007,(OTU_2:0.000000007,OTU_38:0.030038757)0.860:0.000000006)0.799:0.010322779)0.999:0.054793408)0.995:0.037939994,((OTU_40:0.036746419,(OTU_3:0.000000006,OTU_15:0.048600555)0.730:0.002422572)0.992:0.052006245,(((OTU_28:0.000000006,((((OTU_8:0.000000007,OTU_26:0.039668158)0.992:0.058171794,(((OTU_44:0.431891816,OTU_20:0.087273420)0.842:0.074934215,((OTU_45:0.225427475,OTU_24:0.213406872)0.972:0.107393644,(OTU_65:0.323090252,OTU_59:0.128938744)0.903:0.053503914)0.469:0.044803896)0.256:0.046064093,((OTU_5:0.000000007,OTU_18:0.046264531)0.974:0.058184509,(OTU_6:0.000000007,OTU_19:0.045890322)0.797:0.017831029)0.997:0.101410042)0.969:0.067883746)0.990:0.062039729,(OTU_14:0.000000007,(((OTU_62:0.001400378,(OTU_9:0.000000007,OTU_25:0.000000007)0.949:0.068063487)0.903:0.054124751,OTU_55:0.002770174)0.830:0.013064319,OTU_12:0.041163336)1.000:0.083967902)0.963:0.043561117)1.000:0.085639968,OTU_11:0.000000007)1.000:0.127315011)0.999:0.046124874,(OTU_1:0.000000007,OTU_42:0.042015878)0.765:0.000000006)0.971:0.037307077,OTU_70:0.015826282)1.000:0.099109147)0.308:0.013182076)0.921:0.019086489,(OTU_7:0.000000006,(OTU_52:0.018102916,OTU_53:0.020976946)0.985:0.024227705)0.903:0.015356962)0.924:0.026938270,OTU_67:0.000000006)0.993:0.029424143)0.900:0.011283368)0.872:0.013708432);

www/masque/done/filea1a9748bebd0/shaman_otu_table.tsv

+#OTU ID	1ng-25cycles-1_S38	1ng-25cycles-2_S39	1ng-25cycles-3_S40	1ng-30cycles-1_S50	1ng-30cycles-2_S51	1ng-30cycles-3_S52	20ng-20cycles-1_S14	20ng-20cycles-2_S15	20ng-20cycles-3_S16	20ng-25cycles-1_S2	20ng-25cycles-2_S3	20ng-25cycles-3_S4	5ng-25cycles-1_S26	5ng-25cycles-2_S27	5ng-25cycles-3_S28	zero5ng-25cycles-1_S62	zero5ng-25cycles-2_S63	zero5ng-25cycles-3_S64	zero5ng-30cycles-1_S74	zero5ng-30cycles-2_S75	zero5ng-30cycles-3_S76
+OTU_1	20360	31734	26239	39341	51068	34607	43387	51788	45285	45424	38082	46877	29728	34067	36653	43241	45307	31809	49944	29197	12686
+OTU_10	15	0	12	23	4	6	20	20	12	25	1	12	40	0	25	23	4	16	50	8	5
+OTU_11	31	41	19	107	104	55	46	44	33	107	137	82	43	63	44	18	27	20	138	61	18
+OTU_12	81	146	101	305	409	193	177	233	141	336	403	350	167	239	182	128	186	92	378	243	54
+OTU_13	8	5	18	40	8	6	30	27	20	33	1	22	50	6	54	18	0	24	62	19	4
+OTU_14	33	81	36	181	210	103	57	103	59	183	211	175	106	123	112	61	93	26	248	189	24
+OTU_15	24	77	27	101	174	79	39	76	57	100	133	103	66	49	50	52	77	35	71	102	19
+OTU_16	3	1	3	32	1	2	14	11	1	11	8	9	16	7	21	6	1	9	10	13	4
+OTU_17	0	2	0	4	4	0	6	3	2	5	3	1	1	2	6	1	0	2	9	5	0
+OTU_18	24	47	39	86	129	54	35	80	60	82	121	96	38	88	85	53	71	28	85	57	8
+OTU_19	12	37	15	60	83	53	41	54	22	63	91	77	55	70	49	20	49	22	66	59	7
+OTU_2	18676	27903	26126	34853	50574	32174	42742	55406	45490	37495	29397	35607	30330	40305	37747	45089	50059	35897	46262	33097	9973
+OTU_20	0	7	4	10	11	10	0	0	0	0	0	0	0	3	0	14	20	5	16	6	0
+OTU_21	3	1	1	20	5	2	4	6	11	2	8	10	8	8	4	2	3	2	13	6	3
+OTU_22	0	0	0	0	5	1	1	0	2	1	0	5	5	0	0	0	1	1	8	0	1
+OTU_23	5	0	0	4	5	0	0	2	2	4	0	7	5	1	1	0	0	2	5	0	0
+OTU_24	2	4	4	13	5	4	0	0	1	0	1	0	0	2	2	18	6	2	16	8	4
+OTU_25	2	1	1	3	6	1	0	2	1	3	6	6	0	2	7	0	0	0	5	3	0
+OTU_26	26	61	23	103	136	69	30	85	72	114	104	102	50	89	98	43	63	37	120	67	14
+OTU_27	0	0	5	2	0	0	0	2	2	1	0	2	0	0	0	2	0	0	3	0	0
+OTU_28	12	18	13	39	60	38	15	25	22	61	41	54	22	41	16	13	33	6	63	21	9
+OTU_29	0	0	0	3	0	2	0	3	9	2	0	0	4	0	1	4	0	0	2	3	0
+OTU_3	15314	25794	20477	27080	42310	25483	35798	49896	38160	29170	26927	30129	24028	32206	32946	37830	44979	31431	35228	26258	7556
+OTU_30	0	2	0	2	0	0	0	0	0	2	0	3	0	0	1	0	0	0	6	0	0
+OTU_31	2	0	1	1	0	0	0	3	1	1	2	0	0	5	2	0	0	2	0	0	0
+OTU_32	0	0	0	0	3	0	5	1	0	2	0	2	0	0	0	2	0	0	2	0	0
+OTU_33	2	1	0	0	0	1	5	1	2	7	0	1	2	5	0	1	2	2	8	6	1
+OTU_34	2	3	0	2	0	2	1	2	0	1	0	1	0	0	0	0	0	2	2	0	0
+OTU_35	0	0	1	2	0	0	3	3	3	1	2	1	5	2	0	1	0	0	6	3	0
+OTU_36	1	0	0	3	0	0	0	0	2	0	0	2	1	1	2	1	4	2	2	5	0
+OTU_37	0	0	0	3	0	1	0	0	0	0	0	2	0	2	0	1	0	0	1	2	0
+OTU_38	18	49	21	76	100	69	42	57	37	92	102	72	55	87	75	33	69	20	91	65	16
+OTU_39	0	3	0	0	0	0	0	0	0	0	4	1	0	0	1	2	0	0	4	0	0
+OTU_4	16885	29352	20248	35722	51543	31124	43834	49443	39468	39295	32315	31447	31638	39818	43126	48856	47605	32203	48057	32531	7283
+OTU_40	34	71	39	152	211	70	92	144	72	129	144	113	90	124	126	80	109	60	197	91	28
+OTU_41	1	0	0	1	0	1	0	2	0	1	0	0	0	0	1	2	0	0	0	0	0
+OTU_42	122	234	132	459	646	276	214	352	261	426	501	439	250	410	337	201	335	118	554	346	88
+OTU_43	3	8	2	24	21	15	3	9	6	48	33	20	15	6	13	6	3	0	28	19	7
+OTU_44	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	3	4	0	12	0
+OTU_45	0	0	0	0	1	0	0	0	0	0	0	0	3	3	0	0	0	0	5	3	0
+OTU_46	1	2	2	4	7	1	5	0	0	0	6	0	0	1	7	1	4	1	2	4	0
+OTU_47	251	434	240	910	1133	514	426	752	465	976	922	818	459	718	581	386	562	280	1158	758	51
+OTU_48	1	0	0	0	0	0	2	2	0	0	0	0	0	0	0	3	0	0	0	0	0
+OTU_49	286	510	294	1191	1456	598	540	800	498	1240	1044	1044	597	1024	748	435	610	315	1447	815	77
+OTU_5	14126	24363	19543	28630	43085	22741	32492	43287	35159	32594	29854	35222	24098	33055	33176	33168	40478	29085	38149	27187	3814
+OTU_50	0	0	0	0	0	0	0	0	0	5	0	0	0	0	1	1	0	0	0	0	0
+OTU_51	0	0	0	2	0	0	0	0	0	3	0	0	0	0	0	0	0	0	3	0	0
+OTU_52	38	59	28	107	107	54	71	89	47	98	95	118	61	88	70	40	51	20	151	92	7
+OTU_53	79	157	90	345	430	135	164	269	147	350	316	307	175	259	193	112	211	95	435	250	21
+OTU_54	0	0	0	2	0	0	0	0	0	0	0	2	3	0	1	0	0	1	1	0	0
+OTU_55	43	93	43	179	237	168	107	140	120	241	250	230	129	169	142	88	152	47	231	165	24
+OTU_56	0	0	2	0	0	1	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0
+OTU_57	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	0	0	0	0	1
+OTU_58	0	0	0	0	2	0	0	0	0	4	0	2	0	0	0	1	0	0	0	2	0
+OTU_59	0	0	3	1	0	0	0	0	0	0	0	0	0	0	0	6	1	2	6	2	1
+OTU_6	10221	17184	13612	20142	30222	18339	22934	29582	23374	22158	21126	24194	16763	22817	21790	23266	28458	18470	26889	19066	5882
+OTU_60	52	69	40	147	235	118	81	135	97	152	160	189	109	146	88	54	98	44	191	136	50
+OTU_61	5	10	0	24	19	13	7	6	3	20	22	15	6	14	15	2	6	0	38	13	6
+OTU_62	23	94	38	137	188	107	58	89	80	189	143	141	83	130	97	61	75	34	149	123	20
+OTU_63	0	0	0	0	0	0	0	1	0	2	0	0	1	0	1	0	0	2	0	0	0
+OTU_64	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0
+OTU_65	0	0	2	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+OTU_66	104	191	79	439	444	250	168	311	180	365	390	277	203	285	269	139	249	72	427	262	80
+OTU_67	128	216	117	407	543	262	223	311	203	420	398	352	209	278	343	194	282	118	471	296	71
+OTU_68	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+OTU_69	3	2	1	10	9	9	9	9	3	10	8	9	2	10	2	5	9	3	15	7	8
+OTU_7	7592	13857	9387	13681	22111	12021	16756	22535	17609	15537	14537	15067	10473	14958	15970	17494	21041	13521	17356	13458	4075
+OTU_70	4	4	3	43	32	16	1	10	1	37	24	20	3	16	8	5	1	1	30	18	2
+OTU_8	6475	11438	8766	13541	20838	9719	15078	22324	17257	14658	14653	16586	11792	16048	16112	14737	19042	11961	19486	13319	1717
+OTU_9	71	128	63	222	340	161	129	167	103	274	275	208	130	238	183	120	143	68	318	224	39

www/masque/done/filea1a9748bebd0/shaman_process_annotation.tsv

+Type	Count	Mean_length	Median_length
+Amplicon	5667037	429	427
+Dereplication	2807991	429	427
+Singleton_removed	41960	430	427
+Chimera_removed	35606	430	427
+OTU	70	353	424
+silva_annotation	42
+greengenes_annotation	41
+rdp_annotation	69

www/masque/done/filea1a9748bebd0/shaman_process_build.tsv

+sample	Raw_reads_fwd	Raw_mean_length_fwd	Raw_median_length_fwd	Raw_reads_rev	Raw_mean_length_rev	Raw_median_length_rev	Trimmed	Trimmed_fwd	Trimmed_rev	Removed	Removed_fwd	Removed_rev	Filtered_reads_fwd	Filtered_mean_length_fwd	Filtered_median_length_fwd	Filtered_reads_rev	Filtered_mean_length_rev	Filtered_median_length_rev	Combined pairs	Uncombined pairs	Selected_dereplication	Selected_singleton	Selected_chimera	Selected_otu	Mapped_reads	Mapping_percent_combined
+5ng-25cycles-2_S27	284620	300	301	284620	300	300	535653	251625	284028	14	7	7	284613	285	284	284613	279	279	282525	284613	131359	2125	1756	4	238088	83.65
+20ng-20cycles-1_S14	297586	300	301	297586	300	300	561759	264767	296992	4	2	2	297584	285	284	297584	279	279	295212	297584	134679	2100	1886	4	255895	85.99
+20ng-25cycles-3_S4	296908	300	301	296908	300	300	564512	268252	296260	8	4	4	296904	285	284	296904	279	279	294155	296904	141106	2246	1812	5	240633	81.05
+5ng-25cycles-1_S26	216807	300	301	216807	300	300	410968	194591	216377	6	3	3	216804	285	284	216804	279	279	215222	216804	98761	1547	1296	6	182120	84.0
+20ng-25cycles-1_S2	302678	300	301	302678	300	300	577044	274979	302065	13	7	6	302671	285	284	302671	279	279	299987	302671	148426	2291	1814	3	242561	80.14
+zero5ng-25cycles-2_S63	352123	300	301	352123	300	300	659554	308094	351460	4	2	2	352121	286	284	352121	279	279	348756	352121	165806	2592	2317	2	300582	85.36
+zero5ng-25cycles-1_S62	308283	300	301	308283	300	300	581421	273749	307672	6	3	3	308280	285	284	308280	279	279	305526	308280	140665	2110	1940	2	266145	86.33
+1ng-25cycles-2_S39	225513	300	301	225513	300	300	422683	197695	224988	4	2	2	225511	286	284	225511	279	279	222725	225511	116008	1826	1583	3	184494	81.81
+1ng-30cycles-1_S50	275152	300	301	275152	300	300	520299	245752	274547	34	17	17	275134	285	284	275134	279	279	272693	275134	136424	2068	1587	8	219023	79.61
+20ng-25cycles-2_S3	269896	300	301	269896	300	300	510908	241591	269317	8	4	4	269892	285	284	269892	279	279	267249	269892	135359	2156	1676	2	213001	78.92
+1ng-25cycles-1_S38	133794	300	301	133794	300	300	252331	118843	133488	4	2	2	133792	285	284	133792	279	279	132305	133792	66824	1033	915	2	111204	83.12
+zero5ng-25cycles-3_S64	236495	300	301	236495	300	300	445831	209795	236036	5	3	2	236492	285	284	236492	279	279	234247	236492	104951	1692	1581	3	206026	87.12
+20ng-20cycles-2_S15	386487	300	301	386487	300	300	727489	341766	385723	10	5	5	386482	285	284	386482	279	279	383237	386482	179798	2840	2514	2	328702	85.05
+zero5ng-30cycles-3_S76	132333	300	301	132333	300	300	244174	114554	129620	2	1	1	132332	286	284	132332	280	279	118610	132332	110832	428	383	0	53758	40.62
+1ng-25cycles-3_S40	172137	300	301	172137	300	300	324738	152947	171791	2	1	1	172136	285	284	172136	279	279	170386	172136	83061	1292	1175	4	145965	84.8
+zero5ng-30cycles-2_S75	242911	300	301	242911	300	300	461139	218777	242362	14	7	7	242904	285	284	242904	279	279	240422	242904	113875	1744	1430	4	198702	81.8
+zero5ng-30cycles-1_S74	359368	300	301	359368	300	300	682671	324017	358654	45	23	22	359345	285	284	359345	279	279	355985	359345	172641	2623	2030	5	288718	80.35
+20ng-20cycles-3_S16	306702	300	301	306702	300	300	578443	272408	306035	6	3	3	306699	285	284	306699	279	279	303921	306699	135634	2066	1881	1	264662	86.29
+1ng-30cycles-2_S51	391843	300	301	391843	300	300	739590	348609	390981	10	5	5	391838	285	284	391838	279	279	388256	391838	191024	3020	2504	4	319274	81.48
+5ng-25cycles-3_S28	285903	300	301	285903	300	300	540819	255475	285344	4	2	2	285901	285	284	285901	279	279	283559	285901	127824	1980	1635	4	241584	84.5
+1ng-30cycles-3_S52	256766	300	301	256766	300	300	481510	225448	256062	6	3	3	256763	286	284	256763	279	279	252059	256763	172934	2181	1891	2	189728	73.89

www/masque/done/filea1a9748bebd0/shaman_silva_annotation.tsv

+OTU	Kingdom	Phylum	Class	Order	Family	Genus	Specie
+OTU_25	Bacteria	Firmicutes					
+OTU_59	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas	Sphingomonas sp.
+OTU_40	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria	
+OTU_9	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+OTU_62	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia-Shigella	
+OTU_60	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Fastidiosipila	
+OTU_2	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_5	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	Salmonella enterica subsp. enterica serovar Agona str. 47.E.09
+OTU_45	Bacteria	Cyanobacteria	Melainabacteria	Obscuribacterales			
+OTU_44	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Muribaculaceae		
+OTU_19	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia-Shigella	
+OTU_20	Bacteria	Proteobacteria	Gammaproteobacteria	Betaproteobacteriales	Burkholderiaceae	Pelomonas	uncultured Comamonadaceae bacterium
+OTU_3	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria	Listeria monocytogenes
+OTU_47	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria	
+OTU_14	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae		
+OTU_70	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_18	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	
+OTU_4	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_65	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Sneathia	
+OTU_8	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
+OTU_67	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_6	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia-Shigella	Escherichia coli
+OTU_66	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella	
+OTU_11	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae		
+OTU_28	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
+OTU_49	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_15	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria	
+OTU_1	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	Lactobacillus sp. 2011_Ileo_VSA_C5
+OTU_26	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
+OTU_41	Eukaryota	Fungi	Tremellomycetes	Tremellales	Cryptococcaceae	Cryptococcus	Cryptococcus neoformans var. neoformans B-3501A
+OTU_69	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_12	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae		
+OTU_55	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae		
+OTU_61	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_7	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	Enterococcus faecalis
+OTU_24	Bacteria	Actinobacteria	Actinobacteria	Propionibacteriales	Propionibacteriaceae	Cutibacterium	Cutibacterium acnes
+OTU_46	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae		
+OTU_53	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_52	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+OTU_38	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	
+OTU_43	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
+OTU_42	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	

www/masque/done/filea1a9748bebd0/shaman_silva_tree.nhx

+(OTU_43:0.043065538,(OTU_4:0.000000007,OTU_46:0.009499885)0.925:0.018605697,(OTU_49:0.020643917,(((OTU_40:0.036758939,(OTU_3:0.000000007,OTU_15:0.049180884)0.733:0.002875830)0.991:0.039579799,((OTU_66:0.017902335,(OTU_61:0.050068509,((OTU_69:0.000000007,OTU_60:0.039615642)0.000:0.000000007,(OTU_2:0.000000007,OTU_38:0.030429043)0.000:0.000000007)0.705:0.006231766)0.986:0.041162159)0.000:0.029462530,(((OTU_14:0.000000007,(((OTU_8:0.000000007,OTU_26:0.039942502)0.988:0.056796602,((OTU_20:0.146385742,((OTU_65:0.326111890,OTU_59:0.133033691)0.882:0.051081053,(OTU_44:0.414762963,(OTU_45:0.236062817,OTU_24:0.201453677)0.514:0.045175108)0.901:0.080591364)0.201:0.041178794)0.912:0.057034587,((OTU_5:0.000000006,OTU_18:0.046682783)0.975:0.058197730,(OTU_6:0.000000007,OTU_19:0.046385742)0.804:0.018453808)0.997:0.102953636)0.974:0.067491668)0.992:0.065261015,OTU_11:0.086703754)0.882:0.043661284)0.872:0.050119101,(_R_OTU_41:1.823998631,(((OTU_62:0.002081216,(OTU_9:0.000000007,OTU_25:0.000000007)0.950:0.068029812)0.971:0.053834779,OTU_55:0.003022945)0.646:0.006742090,OTU_12:0.047049095)0.000:0.021518168)0.557:0.021182743)1.000:0.177012761,(OTU_70:0.000000007,(OTU_28:0.046271013,(OTU_1:0.000000007,OTU_42:0.042679568)0.000:0.000000007)0.993:0.051799927)0.996:0.088730473)0.551:0.021344639)0.895:0.026850633)0.646:0.032331834,((OTU_67:0.000000007,(OTU_7:0.000000007,(OTU_52:0.018211514,OTU_53:0.021321050)0.987:0.024554344)1.000:0.041446735)0.995:0.030584891,OTU_47:0.022411077)0.000:0.000000007)0.873:0.011411699)0.848:0.014281058);