Commit f5c4129a authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

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
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