Commit f5c4129a authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Add several example dataset and debug the project loading

parent 5d217f8f
Pipeline #14199 passed with stage
in 13 minutes and 30 seconds
*.Rproj.user
*.Rhistory
*.RData
.DS_Store
.Rproj.user
www/masque.png
stages:
- build_conda
- build_dev
- build_master
- build_conda
services:
- docker:dind
......@@ -34,8 +35,7 @@ build_master:
- docker login -u "$DOCKER_USER" -p "$DOCKER_PASS"
- docker build -t aghozlane/shaman .
- docker push aghozlane/shaman
except:
- dev
only:
- master
......@@ -54,6 +54,7 @@ build_conda:
- conda install -y conda-verify
- conda install -y anaconda-client
- conda install -y conda-build
- conda install -y git
script:
- anaconda login --username "$DOCKER_USER" --password "$DOCKER_PASS"
- conda build conda_inst
......
......@@ -1444,10 +1444,10 @@ shinyServer(function(input, output,session) {
reset("fileBiom")
reset("fileTree")
#PS = Project_status(values$masque_key,values$curdir)
values$biom_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva.biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva_tree.nhx",sep=""),sep= .Platform$file.sep)
values$biom_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_",DemoDataset[[1]][2],".biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_",DemoDataset[[1]][2],"_tree.nhx",sep=""),sep= .Platform$file.sep)
#sendSweetAlert(messageId="DemoDataset", title = "Success", text = paste("Data of", DemoDataset[[1]][2], "were successfully loaded. You can go to statistical analysis section."), type = "success", html=TRUE)
sendSweetAlert(session, title = "Success", text = paste("Data of", DemoDataset[[1]][2], "were successfully loaded. You can go to statistical analysis section."), type = "success", html=TRUE)
sendSweetAlert(session, title = "Success", text = paste("Data of", DemoDataset[[1]][3], "were successfully loaded. You can go to statistical analysis section."), type = "success", html=TRUE)
removeCssClass(class = 'pwdRED', selector = '#password_home')
addCssClass(class = 'pwdGREEN', selector = '#password_home')
hideElement("masque-form",anim=TRUE)
......@@ -2248,7 +2248,6 @@ shinyServer(function(input, output,session) {
observeEvent(input$confirmTarget,{
target = NULL
values$biom_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva.biom",sep=""),sep= .Platform$file.sep)
# Get the old biom
if (!is.null(values$biom_masque) && file.exists(values$biom_masque)){
tryCatch(read_biom(values$biom_masque)->data,
......
......@@ -522,7 +522,14 @@ function(request) {
selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Project number"="projnum"),selected="fileCounts"),
conditionalPanel(condition="input.FileFormat=='fileCounts'",
checkboxInput("NoTaxoFile","No taxonomy table",value=FALSE),
selectInput("DemoDataset",h6(strong('Or select a dataset')),c("..."="...","ZymoBIOMICS mock 16S"=c("30a47fca2dc3|Volant et al. 2019 in review")),selected="...")#,
selectInput("DemoDataset",h6(strong('Or select a dataset')),
c("..."="...",
"ZymoBIOMICS mock 16S: Volant et al. 2019"=c("a1a9748bebd0|silva|Volant et al. 2019 in review"),
"Afribiota: Vonaesch et al. 2018"=c("1be225fc935c7|silva|Vonaesch et al. 2018"),
"DNA extraction protocols 16S: Angebault et al. 2018"=c("eec74b27d162|silva|Angebault et al. 2018"),
"DNA extraction protocols ITS1: Angebault et al. 2018"=c("3580714197f5|unite|Angebault et al. 2018"),
"Listeria: Quereda et al. 2016"=c("69207712064|silva|Quereda et al. 2016")),
selected="...")#,
#receiveSweetAlert(messageId = "DemoDataset")
),
conditionalPanel(condition="input.FileFormat=='projnum'",
......
{"type": "16S", "phredthres": 20, "annotationstrand": "both", "aFmax": 0.945, "aPmin": 0.75, "aSmin": 0.98, "path": "/tmp/RtmpggfRsE/Masque_files", "aCmin": 0.785, "minreadlength": 50, "mail": "amine.ghozlane@pasteur.fr", "clusteringthreshold": 0.97, "aOmax": 0.865, "host": "hg38", "name": "file1be225fc935c7", "aPmax": 0.785, "clusteringstrand": "both", "minampliconlength": 50, "dreptype": "--derep_prefix", "maxampliconlength": 0, "data_history_name": "data_shaman_2186_108", "aOmin": 0.82, "aGmin": 0.945, "aKmin": 0.75, "aFmin": 0.865, "paired": false, "result_history_name": "shaman_2186_108", "mincorrect": 80, "minabundance": 4, "contaminant": "/tmp/RtmpggfRsE/file1be225fc935c7_contaminant.fasta", "aGmax": 0.98, "aCmax": 0.82}
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Type Count Mean_length Median_length
Amplicon 13259690 246 249
Dereplication 2903184 244 249
Singleton_removed 172297 247 249
Chimera_removed 117742 247 249
OTU 2386 234 249
silva_annotation 2375
greengenes_annotation 2367
rdp_annotation 2385
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{"contaminant": "/tmp/Rtmpimkesv/file873bc712cf0_contaminant.fasta", "data_history_name": "data_shaman_37694_0", "paired": true, "host": "", "type": "16S", "pattern_R1": "_R1", "result_history_name": "shaman_37694_0", "path_R2": "/tmp/Rtmpimkesv/Masque_files_R2", "mail": "amine.ghozlane@pasteur.fr", "name": "file873bc712cf0", "path_R1": "/tmp/Rtmpimkesv/Masque_files_R1"}
\ No newline at end of file
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:18:38","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_11","metadata":["k__Bacteria","p__Cyanobacteria","c__4C0d-2","o__MLE1-12","f__Bacteria","g__Cyanobacteria","s__4C0d-2"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Betaproteobacteria","o__Burkholderiales","f__Comamonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_17","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_18","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_19","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_2","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_20","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_21","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_22","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_23","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_24","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_25","metadata":["k__Bacteria","p__Bacteroidetes","c__Bacteroidia","o__Bacteroidales","f__S24-7","g__Bacteria","s__Bacteroidetes"]},{"id":"OTU_26","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_27","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_28","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_29","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_3","metadata":["k__Bacteria","p__Actinobacteria","c__Actinobacteria","o__Actinomycetales","f__Propionibacteriaceae","g__Propionibacterium","s__acnes"]},{"id":"OTU_30","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_31","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_32","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_33","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_34","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_35","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_36","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_37","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_38","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_39","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_4","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_40","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_41","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_42","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_43","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_44","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_45","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_46","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_47","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_48","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_49","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_5","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_50","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_51","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_52","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_53","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_54","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_55","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_56","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_57","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_58","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_59","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_6","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_60","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_61","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_62","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_63","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_7","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_8","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_9","metadata":["k__","p__","c__","o__","f__","g__","s__"]}],"columns":[{"id":"1ng.25cycles.1_S38_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.2_S39_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.3_S40_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.30cycles.1_S50_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.2_S51_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.3_S52_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"20ng.20cycles.1_S14_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.2_S15_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.3_S16_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.25cycles.1_S2_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.2_S3_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.3_S4_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.1_S26_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.2_S27_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.3_S28_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.1_S62_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.2_S63_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.3_S64_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.30cycles.1_S74_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.2_S75_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.3_S76_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}}],"data":[[17452,27133,22628,34080,44295,26503,37448,44573,39161,39050,32932,40607,25728,29573,31779,37086,38992,27499,43560,25485,6836],[13,0,12,22,3,5,18,18,11,24,1,12,37,0,22,22,4,16,43,8,3],[2,1,3,28,1,2,10,11,1,11,8,8,16,6,20,5,1,9,10,13,3],[11,29,14,55,74,41,35,48,20,45,75,62,49,65,41,18,43,19,52,52,4],[20,40,34,76,116,38,35,70,51,70,113,79,32,74,72,43,64,24,77,48,5],[0,6,3,8,9,8,0,0,0,0,0,0,0,3,0,12,18,5,13,6,0],[23,62,30,79,149,57,39,72,59,86,106,100,62,47,51,51,67,34,63,90,10],[0,2,0,4,4,0,6,3,2,5,3,1,1,2,6,1,0,2,9,5,0],[5,0,0,4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\ No newline at end of file
#OTU ID 1ng-25cycles-1_S38_L001_001 1ng-25cycles-2_S39_L001_001 1ng-25cycles-3_S40_L001_001 1ng-30cycles-1_S50_L001_001 1ng-30cycles-2_S51_L001_001 1ng-30cycles-3_S52_L001_001 20ng-20cycles-1_S14_L001_001 20ng-20cycles-2_S15_L001_001 20ng-20cycles-3_S16_L001_001 20ng-25cycles-1_S2_L001_001 20ng-25cycles-2_S3_L001_001 20ng-25cycles-3_S4_L001_001 5ng-25cycles-1_S26_L001_001 5ng-25cycles-2_S27_L001_001 5ng-25cycles-3_S28_L001_001 zero5ng-25cycles-1_S62_L001_001 zero5ng-25cycles-2_S63_L001_001 zero5ng-25cycles-3_S64_L001_001 zero5ng-30cycles-1_S74_L001_001 zero5ng-30cycles-2_S75_L001_001 zero5ng-30cycles-3_S76_L001_001
OTU_1 17452 27133 22628 34080 44295 26503 37448 44573 39161 39050 32932 40607 25728 29573 31779 37086 38992 27499 43560 25485 6836
OTU_10 13 0 12 22 3 5 18 18 11 24 1 12 37 0 22 22 4 16 43 8 3
OTU_11 2 1 3 28 1 2 10 11 1 11 8 8 16 6 20 5 1 9 10 13 3
OTU_12 11 29 14 55 74 41 35 48 20 45 75 62 49 65 41 18 43 19 52 52 4
OTU_13 20 40 34 76 116 38 35 70 51 70 113 79 32 74 72 43 64 24 77 48 5
OTU_14 0 6 3 8 9 8 0 0 0 0 0 0 0 3 0 12 18 5 13 6 0
OTU_15 23 62 30 79 149 57 39 72 59 86 106 100 62 47 51 51 67 34 63 90 10
OTU_16 0 2 0 4 4 0 6 3 2 5 3 1 1 2 6 1 0 2 9 5 0
OTU_17 5 0 0 4 4 0 0 1 2 4 0 7 5 1 1 0 0 1 5 0 0
OTU_18 3 1 0 14 4 0 4 4 9 2 6 4 6 5 3 1 0 1 8 5 2
OTU_19 1 4 3 10 4 2 0 0 1 0 0 0 0 2 1 14 6 1 15 5 3
OTU_2 15860 23646 22078 29667 43537 24072 36479 47320 38806 32012 25103 30496 26135 34793 32500 38523 42830 30774 39737 28634 4774
OTU_20 0 0 0 0 5 1 1 0 2 1 0 5 4 0 0 0 1 1 7 0 0
OTU_21 13 23 11 54 78 31 13 60 44 66 66 57 22 51 53 22 33 17 61 37 5
OTU_22 10 17 12 34 56 32 14 23 18 55 38 49 20 36 16 13 32 6 53 21 7
OTU_23 0 1 0 4 1 1 0 0 0 2 1 1 7 0 1 3 3 0 2 4 0
OTU_24 0 0 0 3 0 2 0 3 7 2 0 0 4 0 1 3 0 0 2 2 0
OTU_25 18 42 20 68 88 57 37 48 35 86 90 68 52 80 65 32 59 20 80 61 11
OTU_26 1 1 1 7 1 0 0 0 1 0 0 0 5 1 0 2 2 0 3 1 0
OTU_27 1 0 1 1 0 0 0 3 1 1 1 0 0 3 2 0 0 2 0 0 0
OTU_28 0 0 0 2 0 1 0 0 0 0 0 1 0 2 0 1 0 0 1 2 0
OTU_29 1 0 0 0 0 1 4 1 2 3 0 1 1 4 0 1 2 1 7 6 1
OTU_3 13125 22105 17509 23529 36814 19721 30956 43056 33082 25061 23471 26121 20873 27980 28509 32630 38907 27115 30649 23025 3775
OTU_30 2 3 0 2 0 2 1 2 0 1 0 1 0 0 0 0 0 2 2 0 0
OTU_31 1 0 0 2 2 0 0 0 0 2 2 1 0 1 1 0 0 1 4 0 0
OTU_32 31 67 36 143 204 64 86 131 66 124 135 114 86 116 117 74 109 60 189 86 20
OTU_33 111 221 114 414 591 245 197 336 241 391 448 394 231 379 317 186 311 109 506 319 61
OTU_34 0 1 0 0 1 0 0 2 0 0 3 0 2 2 1 2 2 0 2 1 0
OTU_35 0 0 0 0 3 0 4 1 0 2 0 2 0 0 0 0 0 0 2 0 0
OTU_36 0 0 0 0 1 0 0 0 0 0 0 0 2 2 0 0 0 0 4 2 0
OTU_37 1 3 2 4 7 1 5 0 0 0 2 0 0 1 5 1 3 1 2 4 0
OTU_38 225 379 195 805 1014 423 387 669 422 858 826 711 406 628 505 341 511 249 1032 668 30
OTU_39 5 2 1 1 4 3 0 0 0 4 1 0 2 3 4 0 0 0 5 0 0
OTU_4 13337 23359 16051 28762 41768 20948 35150 39582 31692 31582 26212 25297 25494 32339 34775 39042 38318 25859 39136 26583 2790
OTU_40 0 0 5 2 0 0 0 2 2 1 0 2 0 0 0 2 0 0 3 0 0
OTU_41 0 0 0 0 1 0 0 3 1 0 2 0 0 0 0 0 0 1 3 1 0
OTU_42 2 4 1 16 15 8 2 4 5 33 28 9 9 5 8 4 1 0 20 15 3
OTU_43 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 10 0
OTU_44 195 379 163 976 1055 534 504 662 366 1009 867 564 595 730 708 421 503 222 1225 583 85
OTU_45 76 149 84 320 410 129 150 252 132 329 309 278 162 237 190 101 194 94 409 240 22
OTU_46 0 0 0 2 0 0 0 0 0 0 0 1 3 0 1 0 0 1 0 0 0
OTU_47 0 0 2 0 0 1 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0
OTU_48 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2 0 0 0 0 0
OTU_49 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 6 1 1 5 2 0
OTU_5 11531 20057 16044 23534 35804 15246 26747 35766 29197 26834 24773 29176 19939 27576 27496 27523 33651 24155 31504 22764 1540
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0
OTU_52 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 0 0
OTU_53 0 0 1 2 0 0 3 3 3 1 1 1 5 2 0 1 0 0 6 3 0
OTU_54 36 50 24 100 95 47 64 74 46 91 89 111 56 84 59 37 45 20 140 83 3
OTU_55 249 450 266 1061 1311 492 477 712 443 1093 933 930 542 916 663 398 548 274 1285 737 49
OTU_56 1 0 0 2 0 0 0 0 2 0 0 2 1 1 1 1 2 2 2 3 0
OTU_57 41 59 27 171 185 84 54 91 74 173 163 170 95 90 127 30 76 61 200 139 10
OTU_58 5 5 6 17 27 17 11 5 12 25 28 24 15 11 25 3 6 6 45 18 1
OTU_59 1 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 0 0 0
OTU_6 8183 13707 10964 16276 24625 12822 18729 23977 19123 17982 17070 19830 13793 18802 17884 18929 23174 15187 21971 15719 2336
OTU_60 17 44 12 101 137 71 36 100 59 94 86 118 59 90 71 46 51 32 122 72 17
OTU_61 1 1 0 9 6 10 7 5 3 5 6 8 1 8 1 1 5 1 9 4 2
OTU_62 3 3 2 42 29 14 1 9 1 37 24 16 3 15 7 5 1 1 25 12 2
OTU_63 0 2 0 2 0 0 0 0 0 0 0 3 0 0 1 0 0 0 6 0 0
OTU_7 6506 11883 8080 11966 19193 9309 14386 19327 15146 13448 12560 13118 9135 12995 13890 15038 18146 11681 15168 11666 2165
OTU_8 5082 9047 7033 10887 16871 6722 12362 18325 14321 11921 11802 13621 9812 13294 13394 12133 15601 9962 15972 11023 651
OTU_9 7 5 17 39 8 6 29 26 19 32 1 22 47 6 51 17 0 22 58 17 3
Type Count Mean_length Median_length
Amplicon 4248638 428 427
Dereplication 1629789 428 427
Singleton_removed 40537 429 427
Chimera_removed 34496 429 427
OTU 63 354 427
silva_annotation 39
greengenes_annotation 39
rdp_annotation 62
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-1_S26_L001_001 216807 300 301 216807 300 300 403438 196888 206550 27842 17587 10255 192017 265 277 192017 227 231 167270 192017 60409 1507 1277 5 153559 79.97
20ng-25cycles-1_S2_L001_001 302678 300 301 302678 300 300 560043 274679 285364 42410 25097 17313 265513 265 277 265513 224 229 228922 265513 90528 2208 1749 5 202669 76.33
1ng-30cycles-1_S50_L001_001 275152 300 301 275152 300 300 509447 250179 259268 37693 21809 15884 242096 265 277 242096 222 227 209033 242096 84557 1998 1542 7 183410 75.76
zero5ng-25cycles-1_S62_L001_001 308283 300 301 308283 300 300 569407 277786 291621 43427 26767 16660 270219 265 277 270219 225 230 233528 270219 82353 2133 1951 2 222829 82.46
1ng-25cycles-3_S40_L001_001 172137 300 301 172137 300 300 315854 154559 161295 26482 15642 10840 149233 265 277 149233 223 227 128265 149233 48587 1285 1172 1 121491 81.41
5ng-25cycles-3_S28_L001_001 285903 300 301 285903 300 300 531229 257695 273534 37412 25043 12369 252430 264 277 252430 229 234 220357 252430 77958 1986 1662 4 203446 80.6
zero5ng-25cycles-2_S63_L001_001 352123 300 301 352123 300 300 648535 318719 329816 50482 28176 22306 308459 267 277 308459 221 226 266924 308459 98469 2510 2256 2 252325 81.8
zero5ng-25cycles-3_S64_L001_001 236495 300 301 236495 300 300 437038 212481 224557 33097 21161 11936 207488 265 277 207488 227 232 180797 207488 62110 1659 1557 2 173561 83.65
zero5ng-30cycles-1_S74_L001_001 359368 300 301 359368 300 300 665454 326768 338686 49132 28451 20681 316575 266 277 316575 223 227 274564 316575 105773 2526 1974 7 243522 76.92
1ng-25cycles-2_S39_L001_001 225513 300 301 225513 300 300 410838 203514 207324 37100 18912 18188 193922 267 277 193922 218 217 165528 193922 67393 1678 1445 2 152993 78.89
20ng-20cycles-1_S14_L001_001 297586 300 301 297586 300 300 550934 268644 282290 40695 25399 15296 261634 265 277 261634 226 231 226892 261634 79872 2069 1860 3 214491 81.98
1ng-30cycles-3_S52_L001_001 256766 300 301 256766 300 300 453161 223254 229907 58344 31485 26859 206824 257 272 206824 208 205 154532 206824 86516 1969 1688 3 137773 66.61
20ng-25cycles-3_S4_L001_001 296908 300 301 296908 300 300 549201 268361 280840 41730 25666 16064 260316 265 277 260316 226 231 226248 260316 86241 2126 1726 2 202205 77.68
zero5ng-30cycles-2_S75_L001_001 242911 300 301 242911 300 300 449556 221480 228076 33397 18562 14835 213997 267 278 213997 222 227 186286 213997 69094 1759 1455 3 168284 78.64
20ng-25cycles-2_S3_L001_001 269896 300 301 269896 300 300 497132 245483 251649 39492 21246 18246 235824 267 277 235824 221 225 203843 235824 82805 2068 1612 4 178385 75.64
20ng-20cycles-3_S16_L001_001 306702 300 301 306702 300 300 567042 275507 291535 42771 27605 15166 269014 265 277 269014 228 233 234694 269014 80070 2038 1839 3 222691 82.78
zero5ng-30cycles-3_S76_L001_001 132333 300 301 132333 300 300 183132 106023 77109 80943 25722 55221 65823 247 263 65823 174 177 29501 65823 23219 370 323 1 25229 38.33
20ng-20cycles-2_S15_L001_001 386487 300 301 386487 300 300 714269 350082 364187 53920 31621 22299 339401 266 277 339401 223 228 293514 339401 106564 2767 2482 3 275380 81.14
1ng-30cycles-2_S51_L001_001 391843 300 301 391843 300 300 724875 357756 367119 53718 28996 24722 345232 267 277 345232 221 226 299176 345232 117753 2869 2373 3 268610 77.81
5ng-25cycles-2_S27_L001_001 284620 300 301 284620 300 300 528610 259384 269226 36853 21459 15394 252210 267 277 252210 224 229 219794 252210 80454 2038 1683 1 201061 79.72
1ng-25cycles-1_S38_L001_001 133794 300 301 133794 300 300 245147 120830 124317 20848 11371 9477 115918 265 277 115918 220 223 98970 115918 39064 974 870 0 92208 79.55
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:17:11","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Sphingomonas","s__Sphingomonas sp."]},{"id":"OTU_11","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria marthii"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Cyanobacteria","c__Melainabacteria","o__Obscuribacterales","f__Bacteria","g__Cyanobacteria","s__Melainabacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Brochothrix sp. TM5_5"]},{"id":"OTU_17","metadata":["k__Bacteria","p__Bacteroidetes","c__Bacteroidia","o__Bacteroidales","f__Muribaculaceae","g__Bacteria","s__Bacteroidetes"]},{"id":"OTU_18","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Bacteria"]},{"id":"OTU_19","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_2","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_20","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_21","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus fermentum"]},{"id":"OTU_22","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_23","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_24","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_25","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_26","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Escherichia coli"]},{"id":"OTU_27","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia-Shigella","s__Escherichia coli"]},{"id":"OTU_28","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Terribacillus","s__Terribacillus aidingensis"]},{"id":"OTU_29","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__uncultured Bacillus sp."]},{"id":"OTU_3","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacillus acidicola"]},{"id":"OTU_30","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella sp."]},{"id":"OTU_31","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Betaproteobacteriales","f__Burkholderiaceae","g__Pelomonas","s__uncultured Comamonadaceae bacterium"]},{"id":"OTU_32","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus sp. 2011_Ileo_VSA_C5"]},{"id":"OTU_33","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Lactobacillus sp. 2011_Ileo_VSA_C5"]},{"id":"OTU_34","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Enterococcus faecalis"]},{"id":"OTU_35","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Staphylococcus aureus"]},{"id":"OTU_36","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Staphylococcus aureus"]},{"id":"OTU_37","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Enterococcus faecalis"]},{"id":"OTU_38","metadata":["k__Bacteria","p__Actinobacteria","c__Actinobacteria","o__Propionibacteriales","f__Propionibacteriaceae","g__Cutibacterium","s__Cutibacterium acnes"]},{"id":"OTU_39","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_4","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria monocytogenes"]},{"id":"OTU_40","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_41","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_42","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Bacteria"]},{"id":"OTU_43","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacillus sp. 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\ No newline at end of file
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(OTU_412:0.000000008,((OTU_207:0.077831082,OTU_301:0.000000008)0.993:0.113668701,OTU_402:0.031606536)0.883:0.049828591,(OTU_135:0.000000008,((((OTU_423:0.093074135,OTU_69:0.000000008)0.857:0.197101567,(OTU_370:0.116397760,(OTU_191:0.075077752,OTU_144:0.030948531)0.038:0.000000036)0.485:0.057497533)0.610:0.015041579,(OTU_92:0.081150552,OTU_209:0.000000008)0.432:0.000000008)0.741:0.020142747,((OTU_10:0.000000008,OTU_418:0.000000008)0.400:0.011364528,(((OTU_261:0.000000008,((((OTU_111:0.000000008,((OTU_333:0.000000008,(OTU_442:0.050805055,OTU_441:0.058863453)0.848:0.035897256)0.992:0.112155272,(((OTU_347:0.000000008,(OTU_13:0.000000008,OTU_312:0.000000008)0.696:0.000000008)0.348:0.000000008,(OTU_274:0.041372767,(OTU_409:0.000000014,OTU_248:0.286820477)0.591:0.063127530)0.000:0.000000008)0.854:0.028624537,(OTU_7:0.000000008,(OTU_391:0.040780646,OTU_309:0.032601524)0.000:0.000000008)0.750:0.011453263)0.893:0.050458539)0.902:0.067941704)0.000:0.000000008,((OTU_34:0.015495917,((OTU_434:0.109647396,OTU_194:0.000000008)0.999:0.523275974,OTU_107:0.623456071)0.730:0.085458338)0.763:0.052170017,((OTU_128:0.000000008,OTU_35:0.042266381)0.727:0.000000008,(OTU_20:0.012960096,OTU_102:0.112523342)0.715:0.013363638)0.900:0.072685686)0.646:0.022099067)0.940:0.047376749,(OTU_267:0.139014502,((((OTU_116:0.617103151,(((OTU_147:0.416665453,(((OTU_16:0.041613373,(OTU_127:0.019975536,OTU_53:0.033613118)1.000:0.303625511)0.950:0.065588314,OTU_60:0.022244573)0.689:0.022944336,OTU_62:0.000000008)0.998:0.597547182)0.268:0.063399682,(OTU_22:0.121437325,OTU_426:0.149466113)0.725:0.220256342)0.836:0.169476609,(OTU_81:0.631440199,((((((OTU_82:0.467343823,(OTU_159:0.197269431,OTU_433:0.503178478)0.352:0.159657597)0.106:0.039500148,(OTU_458:0.000000027,(((OTU_338:0.000000008,((((OTU_178:0.000000008,(OTU_26:0.000000008,(OTU_77:0.019308124,OTU_167:0.008502073)0.727:0.000000008)0.996:0.051576233)0.548:0.011580741,(((OTU_272:0.017517022,OTU_19:0.024133825)0.000:0.000000008,(OTU_106:0.000000008,OTU_145:0.038904277)0.129:0.000000008)0.938:0.040273553,((OTU_74:0.035235884,OTU_152:0.041807110)0.789:0.015302187,OTU_184:0.028577281)0.589:0.003228241)0.845:0.023277655)0.020:0.007697116,OTU_98:0.000000008)0.018:0.000000036,(OTU_405:0.017014794,OTU_142:0.016949708)0.888:0.024267267)0.918:0.038022298)0.763:0.009884050,(OTU_247:0.000000008,OTU_112:0.000000008)0.992:0.066281063)0.000:0.000000008,(OTU_105:0.000000014,(OTU_340:0.091394487,OTU_30:0.000000008)1.000:0.181700187)0.415:0.042170772)0.999:0.540383381)0.990:0.579689987)0.713:0.092300461,(OTU_55:0.160571978,OTU_168:0.129818114)0.996:0.324589418)0.528:0.040941594,(OTU_322:0.075420438,OTU_54:0.000000008)1.000:0.501446988)0.658:0.088208497,(OTU_44:0.592446862,(OTU_231:0.723470668,(((((OTU_124:0.250103293,OTU_33:0.208790528)0.881:0.100347012,(OTU_29:0.099456052,OTU_163:0.074547179)0.997:0.159629528)0.265:0.028538578,OTU_189:0.184499742)0.587:0.038898964,(((((OTU_85:0.110773022,OTU_79:0.169632240)0.472:0.042819219,((OTU_109:0.120166331,OTU_94:0.025805725)0.701:0.039059029,(OTU_351:0.059511184,((OTU_137:0.114853101,(OTU_174:0.097309682,(OTU_63:0.000000008,OTU_374:0.026875215)0.749:0.014703334)0.926:0.050772797)0.318:0.041823439,OTU_48:0.153082847)0.909:0.065926552)0.944:0.071084927)0.431:0.040282907)0.073:0.019828387,((((OTU_70:0.042454338,OTU_113:0.024444641)0.126:0.002346840,(((((OTU_41:0.000000008,OTU_45:0.091176552)0.000:0.000000008,OTU_429:0.018174937)0.813:0.015556854,(OTU_1:0.005696122,(OTU_103:0.020486007,OTU_78:0.019001589)0.558:0.015238299)0.784:0.014350973)0.882:0.028750366,(OTU_138:0.092656970,OTU_14:0.000000008)0.868:0.016371884)0.942:0.046368266,(OTU_64:0.000000019,OTU_164:0.042406208)0.995:0.072148974)0.826:0.019331122)0.804:0.033066495,OTU_132:0.092216709)0.818:0.032767797,OTU_71:0.153444076)0.521:0.010345099)0.998:0.164233508,(((OTU_59:0.270959236,((((OTU_459:0.044077926,OTU_18:0.000000008)0.939:0.028195486,OTU_266:0.000000008)0.914:0.027729038,(OTU_57:0.017025436,OTU_148:0.114367836)0.670:0.024470491)0.863:0.031825547,OTU_205:0.013250424)0.996:0.242885772)0.736:0.065625572,((OTU_392:0.568585098,(OTU_27:0.107204267,OTU_250:0.000000008)0.749:0.226834965)0.552:0.176752928,OTU_80:0.326162576)0.725:0.082824996)0.928:0.120277567,(OTU_123:0.190317115,OTU_171:0.213485761)0.992:0.274081492)0.881:0.065281879)0.771:0.039602385,(OTU_465:0.147669073,((OTU_169:0.035255532,OTU_255:0.002851078)0.997:0.201977300,(OTU_327:0.432028796,OTU_67:0.104475966)0.516:0.207848633)0.647:0.096544181)0.146:0.069922583)0.287:0.025480556)0.777:0.068558030,((OTU_292:0.409651670,OTU_305:0.137761849)0.950:1.030620251,OTU_456:0.000000008)0.664:0.271821846)0.710:0.055964943)0.737:0.139942539)0.814:0.114858584)0.390:0.030521144,(OTU_151:0.009695720,(OTU_389:0.034370144,OTU_89:0.000000008)0.923:0.066360275)1.000:0.457530321)0.467:0.080287637)0.630:0.129126122)0.569:0.047879334)0.857:0.157470403,((OTU_359:0.000000019,(OTU_31:0.014902062,OTU_110:0.004388430)0.537:0.042465871)0.993:0.348954189,(OTU_280:0.505141807,OTU_84:0.356987644)0.780:0.167376050)0.820:0.187519034)0.789:0.098675556,((OTU_427:0.041546603,(OTU_39:0.000000008,OTU_175:0.018880327)0.537:0.000000008)0.998:0.427440694,(OTU_445:0.018762790,(OTU_224:0.116026187,(((OTU_212:0.021784790,OTU_384:0.008834193)0.878:0.016237722,OTU_269:0.002159690)0.534:0.012160340,((OTU_4:0.009968032,OTU_157:0.005095271)0.000:0.000000008,((OTU_146:0.017468538,OTU_438:0.033055117)0.093:0.008776154,OTU_297:0.057939304)0.000:0.000000036)0.742:0.004902002)0.812:0.051073587)0.791:0.075513060)0.700:0.077619811)0.991:0.344921977)0.922:0.163104862,OTU_385:0.047883640)0.654:0.039440537)0.119:0.000000014)0.961:0.000000008,OTU_9:0.000000008)0.942:0.000000008)0.799:0.000000008,OTU_96:0.079214190)0.880:0.090315047,OTU_294:0.143342973)0.706:0.025991863)0.884:0.020067318)0.790:0.010148617)0.956:0.020822500);
This diff is collapsed.
#OTU ID IHMS1 IHMS2 IHMS3 IHMS4 IHMS5 IHMS6 MOBIO1 MOBIO2 MOBIO3 MOBIO4 MOBIO5 MOBIO6
OTU_1 0 112 3 0 4384 2845 0 85 6 1 3044 13479
OTU_10 0 0 0 0 843 626 0 0 0 0 769 394
OTU_100 0 0 0 0 0 0 0 4 79 44 0 1
OTU_101 26 0 0 0 0 0 51 0 0 0 0 0
OTU_102 0 0 0 0 72 37 0 0 0 0 63 69
OTU_103 0 3 0 0 5 10 0 1 0 0 13 48
OTU_104 0 0 0 1 0 0 0 0 5 56 0 0
OTU_105 0 0 54 0 1 0 0 0 0 0 0 0
OTU_106 0 0 0 0 64 3 0 0 0 0 0 0
OTU_107 0 27 0 0 0 0 0 129 0 0 0 0
OTU_108 0 0 47 0 0 0 0 0 0 0 16 0
OTU_109 0 44 0 0 0 0 1 50 0 0 0 0
OTU_11 6 0 516 676 3 37 27 64 309 642 30 34
OTU_110 31 30 0 0 0 0 0 76 0 0 0 0
OTU_111 0 0 0 0 41 19 0 0 0 0 17 5
OTU_112 0 0 0 0 0 1 0 0 42 0 0 0
OTU_113 0 0 0 0 0 0 0 64 0 0 0 0
OTU_114 144 3 16 12 15 18 0 0 0 2 0 1
OTU_115 0 0 0 69 0 0 0 0 7 0 0 0
OTU_116 0 107 0 0 0 0 0 0 0 0 0 0
OTU_117 0 0 36 50 0 0 2 0 6 0 0 0
OTU_118 0 0 64 103 0 0 0 0 6 17 0 0
OTU_119 58 0 0 0 0 0 56 18 0 0 0 0
OTU_12 1040 491 0 0 0 0 966 817 0 0 0 0
OTU_120 0 0 0 0 0 0 0 41 0 0 0 0
OTU_121 0 0 0 0 27 21 0 0 0 0 4 5
OTU_122 0 0 30 0 0 0 0 0 0 34 0 0
OTU_123 0 87 0 0 0 0 0 0 0 0 0 0
OTU_124 0 0 0 0 0 0 0 58 0 0 0 0
OTU_125 74 24 0 0 0 0 85 101 0 0 0 0
OTU_126 84 0 0 0 0 0 12 2 0 0 0 0
OTU_127 0 0 0 0 0 0 0 70 0 0 0 0
OTU_128 0 0 0 0 35 34 0 0 0 0 68 27
OTU_129 58 0 0 0 0 0 4 14 0 0 0 0
OTU_13 0 0 0 0 386 385 0 0 1 0 1040 286
OTU_130 12 0 25 0 0 0 0 1 0 0 0 0
OTU_131 6 0 91 180 5 15 0 15 14 16 0 0
OTU_132 0 0 56 0 0 0 0 0 0 0 0 0
OTU_133 0 0 12 2 0 0 0 0 7 16 0 0
OTU_134 0 0 2 0 0 0 0 0 0 57 0 0
OTU_135 0 0 0 0 90 38 0 0 0 0 37 56
OTU_136 0 0 0 0 0 0 61 0 0 0 0 0
OTU_137 0 0 0 0 0 0 0 45 0 0 0 0
OTU_138 3 14 0 0 1 2 0 27 0 1 11 13
OTU_139 1 0 84 19 5 0 0 0 5 0 0 0
OTU_14 156 811 0 0 60 182 0 1547 14 24 305 208
OTU_140 0 0 0 0 20 8 0 0 0 0 4 0
OTU_141 0 0 36 0 0 0 0 0 5 25 0 0
OTU_142 0 1 0 0 2 0 0 0 0 0 0 29
OTU_143 4 0 3 3 0 0 7 0 22 4 4 0
OTU_144 0 0 0 0 4 5 0 0 0 0 54 4
OTU_145 0 0 53 2 646 9 0 0 0 0 4 0
OTU_146 131 768 21 0 0 29 275 117 2 24 0 0
OTU_147 0 0 0 0 0 0 0 80 0 0 0 0
OTU_148 0 0 0 0 0 0 0 44 0 0 0 0
OTU_149 0 0 0 0 0 0 59 0 0 0 0 0
OTU_15 1268 0 0 0 0 0 2 0 0 0 0 0
OTU_150 0 0 53 0 0 0 0 0 0 14 0 0
OTU_151 0 0 0 0 0 0 0 0 70 0 0 0
OTU_152 1 0 2 0 5 3 0 0 1 50 1 1
OTU_153 0 0 14 12 1 1 0 0 2 14 4 1
OTU_154 0 0 38 9 0 0 0 0 0 0 0 0
OTU_155 37 0 0 0 0 0 0 0 0 0 0 0
OTU_156 0 0 51 264 0 0 0 0 0 14 0 0
OTU_157 110 502 20 0 0 16 177 71 1 14 0 0
OTU_158 15 0 0 4 5 3 0 0 9 38 8 0
OTU_159 0 0 0 0 0 0 0 0 0 49 0 0
OTU_16 0 0 2051 1 0 0 0 0 0 0 0 0
OTU_160 0 0 0 0 61 2 0 0 0 0 23 5
OTU_161 60 1 0 0 0 0 8 1 0 0 0 0
OTU_162 0 0 124 14 0 0 0 0 7 1 0 0
OTU_163 0 45 0 0 0 0 0 0 0 0 0 0
OTU_164 0 40 0 0 5 0 0 2 0 0 0 0
OTU_165 0 0 0 0 0 34 0 0 0 0 0 0
OTU_166 0 0 31 0 0 0 0 0 0 0 0 0
OTU_167 0 0 0 0 2 312 0 1 0 0 3 0
OTU_168 0 0 0 0 0 0 0 0 61 0 0 0
OTU_169 0 0 0 0 0 0 0 108 0 0 0 1
OTU_17 0 0 0 0 341 511 0 0 0 0 920 83
OTU_170 61 3 45 145 13 14 0 0 19 22 0 0
OTU_171 0 0 0 0 0 0 0 39 0 0 0 0
OTU_172 36 0 0 0 0 0 0 0 0 0 0 0
OTU_173 0 0 22 13 0 0 0 0 6 2 0 0
OTU_174 3 3 0 0 0 0 0 26 0 0 0 0
OTU_175 1 72 0 0 0 0 2 5 0 0 0 0
OTU_176 52 0 5 0 0 0 3 0 0 4 0 0
OTU_177 0 0 0 0 0 0 0 0 4 23 0 0
OTU_178 0 0 44 263 53 12 0 0 2 8 4 2
OTU_179 0 0 0 0 0 0 0 379 0 0 0 0
OTU_18 0 67 0 0 0 0 355 392 224 292 0 0
OTU_180 11 0 0 0 0 0 46 2 0 0 0 0
OTU_181 0 0 19 0 0 0 0 0 1 0 0 0
OTU_182 9 0 0 0 1 0 0 5 0 0 2 0
OTU_183 0 0 0 0 0 0 0 0 0 22 0 0
OTU_184 41 0 0 0 5 0 0 0 0 0 0 0
OTU_185 1 0 0 0 0 0 20 0 0 0 0 0
OTU_186 29 0 0 0 0 0 0 0 8 0 0 0
OTU_187 0 0 0 0 0 0 0 0 29 0 0 0
OTU_188 0 0 15 0 0 0 0 0 26 2 0 0
OTU_189 0 0 0 0 0 0 0 0 22 0 0 0
OTU_19 0 1 15 0 161 0 0 0 0 0 0 0
OTU_190 0 0 0 0 0 0 0 0 0 40 0 0
OTU_191 0 0 0 0 0 0 0 0 0 0 37 0
OTU_192 0 0 26 58 0 0 0 1 94 167 0 0
OTU_193 0 0 0 0 0 1 10 0 0 0 116 8
OTU_194 0 0 0 0 35 59 0 0 0 0 0 17
OTU_195 0 0 10 37 0 0 0 0 6 12 0 0
OTU_196 0 0 0 0 0 0 0 0 0 28 0 0
OTU_197 0 0 0 0 21 22 0 0 0 0 3 2
OTU_198 9 0 0 0 0 0 0 17 0 0 0 0
OTU_199 13 0 0 0 0 0 0 0 0 0 0 0
OTU_2 0 1 1323 2312 0 0 0 171 7053 6619 0 0
OTU_20 0 0 0 0 673 363 0 0 0 0 709 527
OTU_200 0 0 0 27 0 0 0 0 0 0 0 0
OTU_201 139 0 4 0 3 0 0 0 1 6 0 0
OTU_202 1 3 4 5 0 0 0 0 9 6 0 0
OTU_203 0 0 0 0 0 0 0 0 2 2 18 0
OTU_204 0 0 0 62 0 0 0 0 0 0 0 0
OTU_205 0 25 0 0 0 0 0 0 1 1 0 0
OTU_206 0 0 0 0 0 0 0 0 0 18 0 0
OTU_207 0 0 0 0 63 1 0 0 0 0 4 6
OTU_208 0 0 17 0 4 0 0 2 4 16 0 0
OTU_209 0 0 0 0 84 27 0 0 0 0 36 37
OTU_21 56 16 220 312 0 2 17 58 20 157 0 0
OTU_210 0 0 1 1 0 1 0 2 29 49 41 1
OTU_211 0 0 33 29 0 0 3 1 7 0 0 0
OTU_212 18 109 1 0 0 3 26 10 0 5 0 0
OTU_213 0 0 0 0 0 0 17 0 0 0 0 0
OTU_214 0 0 0 0 0 0 0 17 0 0 0 0
OTU_215 0 0 0 0 5 4 0 0 0 0 4 5
OTU_216 0 0 0 57 0 0 0 0 6 23 0 0
OTU_217 14 5 0 0 0 0 10 0 0 0 0 0
OTU_218 0 1 0 0 0 0 15 0 0 0 0 0
OTU_219 1 0 24 24 1 0 0 2 4 0 2 0
OTU_22 66 0 133 411 0 0 152 0 0 101 229 0
OTU_220 0 0 0 0 0 0 16 0 0 0 0 0
OTU_221 0 0 7 6 0 1 0 3 10 5 1 0
OTU_222 0 0 42 0 0 0 0 0 0 0 0 0
OTU_223 0 0 11 0 0 0 0 0 0 0 0 0
OTU_224 2 3 0 0 0 29 5 2 0 1 0 0
OTU_225 66 42 114 164 0 0 22 50 264 186 0 0
OTU_226 3 0 1 8 0 0 49 43 28 13 5 1
OTU_227 0 0 0 0 0 0 0 0 0 0 19 0
OTU_228 0 0 40 0 0 0 0 0 0 0 0 0
OTU_229 4 15 0 0 0 0 0 2 0 0 0 0
OTU_23 7 0 0 0 0 0 0 1717 0 0 0 0
OTU_230 0 0 0 15 0 0 0 0 0 0 0 0
OTU_231 0 0 0 0 0 0 0 0 0 53 0 0
OTU_232 7 0 2 14 2 0 0 0 0 0 0 0
OTU_233 0 0 0 0 0 29 0 0 0 0 0 0
OTU_234 0 0 0 0 0 0 0 0 11 0 0 0
OTU_235 0 0 0 0 9 0 0 0 0 0 3 14
OTU_236 4 0 0 1 1 0 24 4 2 2 0 0
OTU_237 5 4 1 0 0 2 0 11 0 0 1 0
OTU_238 0 0 20 0 2 0 0 0 2 1 0 0
OTU_239 0 0 0 16 0 0 0 0 1 0 0 0
OTU_24 895 42 0 0 0 0 2172 1591 0 0 0 0
OTU_240 0 3 51 0 0 6 0 2 6 1 0 1
OTU_241 0 0 0 0 2 29 0 0 0 0 0 2
OTU_242 12 0 0 0 0 0 0 0 0 0 0 0
OTU_243 21 0 0 0 0 0 0 0 0 0 0 0
OTU_244 0 0 0 0 27 2 0 0 0 0 6 0
OTU_245 0 0 0 0 0 0 0 0 5 23 0 0
OTU_246 0 2 0 0 0 0 0 0 13 7 0 0
OTU_247 0 0 0 0 3 6 0 0 25 0 3 0
OTU_248 0 0 0 0 4 9 0 0 0 0 4 0
OTU_249 0 0 18 0 0 0 0 0 0 0 0 0
OTU_25 0 0 0 0 569 12 0 0 0 0 0 4
OTU_250 0 0 0 11 0 0 0 9 1 4 0 0
OTU_251 16 4 0 0 0 0 2 2 0 0 0 0
OTU_252 0 0 0 16 0 0 0 0 0 0 0 0
OTU_253 1 0 33 5 1 0 0 0 2 0 0 0
OTU_254 0 0 0 0 0 0 0 0 0 0 35 0
OTU_255 0 0 0 0 0 0 0 14 0 0 0 0
OTU_256 6 0 13 82 0 11 0 0 11 9 2 1
OTU_257 0 0 0 0 0 0 10 1 0 0 0 0
OTU_258 5 6 0 0 0 0 0 0 0 0 0 0
OTU_259 18 0 0 17 1 0 61 2 0 1 0 0
OTU_26 0 0 0 1 0 532 0 0 0 0 0 0
OTU_260 0 0 26 0 0 0 0 0 0 0 0 0
OTU_261 0 0 0 0 24 3 0 0 0 0 0 6
OTU_262 0 0 0 0 0 0 0 0 9 0 0 0
OTU_263 0 0 0 3 0 0 33 0 2 0 0 0
OTU_264 0 0 0 0 0 6 0 0 14 0 0 0
OTU_265 0 0 0 0 0 0 0 0 10 0 0 0
OTU_266 0 1 0 0 0 0 3 7 4 1 0 0
OTU_267 0 0 0 0 0 16 0 0 0 0 0 0
OTU_268 0 0 3 2 0 0 2 1 6 1 0 0
OTU_269 8 20 1 0 0 1 10 2 0 0 0 0
OTU_27 0 0 0 332 0 0 0 348 69 167 0 0
OTU_270 0 3 9 10 0 0 0 0 0 0 0 0
OTU_271 0 0 17 3 0 0 0 0 1 0 0 0
OTU_272 0 1 0 0 850 0 0 0 0 0 0 0
OTU_273 25 19 0 0 0 0 22 23 0 0 0 0
OTU_274 0 0 0 0 61 44 0 0 0 0 72 50
OTU_275 0 3 0 0 0 4 0 31 1 0 0 0
OTU_276 3 0 0 17 0 0 0 0 0 0 0 0
OTU_277 0 0 0 11 0 0 0 0 0 17 0 0
OTU_278 0 0 0 0 0 0 0 0 8 4 0 0
OTU_279 0 0 0 13 0 0 0 0 0 0 0 0
OTU_28 13 5 0 0 0 0 716 488 0 0 0 0
OTU_280 0 0 0 0 0 0 0 0 15 0 0 0
OTU_281 0 0 0 0 0 0 0 0 6 12 0 0
OTU_282 0 0 46 0 0 0 0 0 0 0 0 0
OTU_283 0 0 0 0 0 0 11 0 0 0 0 0
OTU_284 0 0 0 0 0 0 0 9 0 0 0 0
OTU_285 0 0 0 23 0 0 0 0 0 0 0 0
OTU_286 0 0 7 0 0 0 0 0 0 0 0 0
OTU_287 5 2 0 0 0 0 3 21 0 0 0 0
OTU_288 0 8 0 0 0 0 0 0 0 0 0 0
OTU_289 0 0 0 0 0 0 0 0 11 1 0 0
OTU_29 0 0 0 0 0 0 0 0 20 690 0 0
OTU_290 20 0 0 0 0 0 0 0 0 0 0 0
OTU_291 0 0 8 0 0 0 0 0 0 2 0 0
OTU_292 0 0 0 0 2 11 0 0 0 0 0 0
OTU_293 0 0 0 0 20 0 0 0 0 0 3 2
OTU_294 0 0 0 0 22 1 0 0 0 0 0 0
OTU_295 0 0 0 0 12 0 0 0 0 0 0 0
OTU_296 0 0 12 0 0 0 0 0 0 0 0 0
OTU_297 4 15 0 0 0 1 11 2 0 0 0 0
OTU_298 0 0 0 0 0 0 16 0 0 0 0 0
OTU_299 0 0 0 0 0 0 10 0 0 0 0 0
OTU_3 1188 845 2156 3198 0 1 407 1069 5197 3775 3 0
OTU_30 0 0 1 2 1 2 0 0 0 0 441 0
OTU_300 0 8 0 0 0 0 0 0 0 3 0 0
OTU_301 0 0 0 0 0 0 0 0 0 0 0 23
OTU_302 0 0 0 0 0 0 31 0 0 0 0 0
OTU_303 18 0 0 0 0 0 0 0 0 0 0 0
OTU_304 0 0 0 30 0 0 0 0 0 0 0 0
OTU_305 0 0 0 0 0 10 0 0 0 0 0 0
OTU_306 0 0 0 0 3 4 0 0 0 0 4 0
OTU_307 15 0 0 0 0 0 0 2 9 0 0 0
OTU_308 0 0 0 0 0 0 1 15 0 0 0 0
OTU_309 0 0 0 0 4 4 0 0 0 0 14 3
OTU_31 233 228 0 0 0 0 0 372 0 0 0 0
OTU_310 0 0 15 5 0 0 0 0 0 0 0 0
OTU_311 0 0 27 1 7 0 0 0 2 0 0 0
OTU_312 0 0 0 0 46 25 0 0 0 0 60 17
OTU_313 23 0 0 0 0 0 0 0 0 0 0 0
OTU_314 0 0 0 0 6 1 0 0 0 0 0 1
OTU_315 0 0 0 0 0 0 0 0 0 0 0 7
OTU_316 0 0 0 0 0 0 0 2 11 0 0 0
OTU_317 0 0 0 0 0 4 0 0 0 0 4 0
OTU_318 0 0 0 0 0 2 0 0 0 0 0 11
OTU_319 3 0 0 0 0 0 5 3 0 0 0 0
OTU_32 0 0 664 459 2 0 0 0 129 114 0 3
OTU_320 0 0 0 7 0 0 0 0 0 0 0 0
OTU_321 0 0 0 0 0 0 0 0 6 0 0 0
OTU_322 0 0 0 0 0 0 0 0 14 0 0 0
OTU_323 0 0 0 0 0 0 0 0 0 9 0 0
OTU_324 18 0 0 0 0 0 0 0 0 0 0 0
OTU_325 0 0 6 0 0 0 0 0 0 0 0 0
OTU_326 0 0 6 2 0 0 0 0 1 0 0 0
OTU_327 0 0 0 0 0 0 0 22 0 0 0 0
OTU_328 0 0 36 0 0 0 0 0 0 0 0 0
OTU_329 0 0 0 0 8 4 0 0 0 0 0 0
OTU_33 0 0 0 513 0 0 0 0 0 0 34 10
OTU_330 0 0 0 0 4 4 0 0 0 0 0 0
OTU_331 0 0 6 16 0 0 0 0 0 0 0 0
OTU_332 0 0 14 0 0 3 7 21 1 0 0 1
OTU_333 0 0 0 0 0 11 0 0 0 0 0 0
OTU_334 0 0 0 1 0 0 0 0 10 0 0 2
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