Add several example dataset and debug the project loading

.gitignore

 *.Rproj.user
 *.Rhistory
 *.RData
+.DS_Store
 .Rproj.user
 www/masque.png

.gitlab-ci.yml

 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

server.R

@@ -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,

ui.R

@@ -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'",

www/masque/done/file1be225fc935c7.json

+{"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}
\ No newline at end of file

www/masque/done/file1be225fc935c7/shaman_process_annotation.tsv

+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

www/masque/done/file30a47fca2dc3.json

-{"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

www/masque/done/file30a47fca2dc3/shaman_otu_table.tsv

-#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

www/masque/done/file30a47fca2dc3/shaman_process_annotation.tsv

-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

www/masque/done/file30a47fca2dc3/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-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

www/masque/done/file30a47fca2dc3/shaman_silva_tree.nhx

-(((OTU_38:0.000000007,(OTU_55:0.024285583,(OTU_58:0.008282235,(OTU_42:0.037715947,(OTU_37:0.009650750,(OTU_4:0.000000007,_R_OTU_23:0.000000007)0.932:0.000000007)0.916:0.015797335)0.891:0.010651872)0.834:0.006653109)0.998:0.031436100)0.999:0.046140362,(OTU_3:0.000000007,(OTU_15:0.040635675,_R_OTU_34:0.000000007)0.736:0.000000007)0.339:0.000000007)0.751:0.003134260,OTU_32:0.036807889,(((OTU_7:0.003251335,(OTU_45:0.020943789,OTU_54:0.018877158)0.957:0.022011936)0.977:0.035446587,((OTU_62:0.005592913,(OTU_33:0.042962896,(OTU_22:0.046702450,(OTU_1:0.000000007,_R_OTU_26:0.000000007)0.619:0.000000007)0.000:0.000000007)0.975:0.046453068)1.000:0.087808386,((OTU_36:0.222083463,((OTU_49:0.157721496,(((OTU_8:0.000000007,OTU_21:0.041004865)0.999:0.126797409,((OTU_12:0.046998885,(OTU_6:0.000000007,_R_OTU_41:0.000000007)0.000:0.000000007)0.801:0.019385127,(OTU_57:0.047097949,(OTU_13:0.047305589,(OTU_5:0.000000007,_R_OTU_31:0.000000007)0.608:0.000000007)0.000:0.000000007)0.964:0.057663607)0.997:0.110114274)0.934:0.062794932,OTU_14:0.125886218)0.837:0.054262608)0.961:0.083615213,(OTU_43:0.411388440,OTU_19:0.236221071)0.157:0.029902162)0.841:0.069591569)0.999:0.177661430,(OTU_44:0.031335407,(OTU_61:0.000000007,(OTU_25:0.030703833,(OTU_2:0.000000007,_R_OTU_39:0.000000007)0.657:0.000000007)0.000:0.000000007)0.828:0.011613514)0.957:0.047175893)0.806:0.024035221)0.915:0.031195289)0.957:0.029474712,OTU_60:0.053031794)0.780:0.012602009);

www/masque/done/file3580714197f5.json

+{"type": "ITS", "phredthres": 20, "annotationstrand": "both", "aFmax": 0.945, "aPmin": 0.75, "aSmin": 0.98, "path": "/tmp/RtmpIsaWzT/Masque_files", "aCmin": 0.785, "minreadlength": 50, "mail": "amine.ghozlane@pasteur.fr", "clusteringthreshold": 0.97, "aOmax": 0.865, "host": "hg38", "name": "file3580714197f5", "aPmax": 0.785, "clusteringstrand": "both", "minampliconlength": 50, "dreptype": "--derep_prefix", "maxampliconlength": 0, "data_history_name": "data_shaman_2186_109", "aOmin": 0.82, "aGmin": 0.945, "aKmin": 0.75, "aFmin": 0.865, "paired": false, "result_history_name": "shaman_2186_109", "mincorrect": 80, "minabundance": 4, "contaminant": "/tmp/RtmpIsaWzT/file3580714197f5_contaminant.fasta", "aGmax": 0.98, "aCmax": 0.82}
\ No newline at end of file

www/masque/done/file3580714197f5/shaman_findley_tree.nhx

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www/masque/done/file3580714197f5/shaman_process_annotation.tsv

+Type	Count	Mean_length	Median_length
+Amplicon	204399	240	249
+Dereplication	33091	253	259
+Singleton_removed	3310	257	261
+Chimera_removed	3238	257	261
+OTU	1	117640	117640
+unite_annotation	166
+findley_annotation	152
+underhill_annotation	144
+rdp_annotation	464

www/masque/done/file3580714197f5/shaman_process_build.tsv

+sample	Raw_reads	Raw_mean_length	Raw_median_length	Trimmed	Removed	Host_1_time	Host_>1_time	Phi_phage_1_time	Phi_phage_>1_time	Filtered_reads	Filtered_mean_length	Filtered_median_length	Selected_dereplication	Selected_singleton	Selected_chimera	Selected_otu	Mapped_reads	Mapping_percent_proc
+MOBIO3	19154	252	256	2469	1757	2	163	0	0	17232	260	271	2714	249	241	0	16635	96.54
+IHMS6	16496	187	160	3104	3232	1	600	0	0	12663	195	160	2016	216	213	0	12281	96.98
+MOBIO5	21236	175	158	3601	3005	2	845	0	0	17384	182	158	2310	248	245	0	16958	97.55
+MOBIO6	25688	207	249	3336	2661	1	1168	0	0	21858	216	249	2178	257	243	0	21467	98.21
+IHMS5	22600	180	159	3890	3798	3	1051	0	0	17748	187	159	2432	275	269	0	17247	97.18
+IHMS3	16067	265	256	3204	1729	2	85	0	0	14251	273	256	2931	287	276	0	13740	96.41
+MOBIO2	21074	259	258	2963	2206	6	271	0	0	18591	266	261	3860	349	344	0	17864	96.09
+IHMS1	19217	256	264	2496	1775	1	157	0	0	17284	263	265	3250	322	314	0	16780	97.08
+MOBIO4	20246	257	273	3007	1683	4	183	0	0	18376	265	279	2963	308	306	0	17967	97.77
+IHMS2	20006	249	272	2258	1681	1	422	0	0	17902	256	272	2494	260	259	0	17682	98.77
+MOBIO1	17162	265	271	2363	1394	3	157	0	0	15608	270	271	2903	262	253	0	15090	96.68
+IHMS4	17333	253	256	3082	1737	2	92	0	0	15502	261	256	3040	277	275	0	15071	97.22

www/masque/done/file3580714197f5/shaman_underhill_tree.nhx

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www/masque/done/file3580714197f5/shaman_unite_tree.nhx

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www/masque/done/file69207712064.json

+{"type": "16S", "path_R2": "/tmp/RtmpBpSnD9/Masque_files_R2", "phredthres": 20, "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/RtmpBpSnD9/file69207712064_contaminant.fasta", "name": "file69207712064", "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_111", "minoverlap": 10, "aOmin": 0.82, "aGmin": 0.945, "path_R1": "/tmp/RtmpBpSnD9/Masque_files_R1", "aFmin": 0.865, "paired": true, "result_history_name": "shaman_2186_111", "mincorrect": 80, "minabundance": 4, "host": "hg38", "aGmax": 0.98, "aCmax": 0.82}
\ No newline at end of file

www/masque/done/file69207712064/shaman_process_annotation.tsv

+Type	Count	Mean_length	Median_length
+Amplicon	1466288	521	525
+Dereplication	904614	521	525
+Singleton_removed	19871	520	525
+Chimera_removed	15061	520	525
+OTU	529	468	519
+silva_annotation	490
+greengenes_annotation	459
+rdp_annotation	528

www/masque/done/file69207712064/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	Host_1_time	Host_>1_time	Phi_phage_1_time	Phi_phage_>1_time	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
+Delta-Compl4-52	382421	300	301	382421	300	301	560388	240191	320197	128103	69648	58455	1	4	202	0	279894	275	294	279894	212	216	51912	279894	32488	721	572	17	39182	14.0
+Delta3-45	210885	300	300	210885	300	301	310452	131207	179245	65137	36026	29111	0	4	136	0	158397	277	295	158397	217	222	31791	158397	17784	456	340	12	25609	16.17
+WT3-57	304309	300	301	304309	300	301	449904	197515	252389	100972	52291	48681	1	1	180	0	223500	276	294	223500	205	210	47544	223500	31547	653	465	28	34952	15.64
+Delta-Compl5-71	79038	300	301	79038	300	301	114783	49047	65736	27381	14939	12442	0	1	55	0	57206	274	294	57206	212	216	13893	57206	9006	162	119	2	9630	16.83
+Delta-m7	174333	300	301	174333	300	301	256037	109172	146865	56589	31135	25454	0	3	111	0	128746	274	294	128746	212	216	25343	128746	14571	348	305	25	21469	16.68
+WT4-58	338059	300	301	338059	300	301	497875	214611	283264	111649	60346	51303	0	4	208	0	248283	274	294	248283	212	216	75138	248283	46778	1049	725	18	52820	21.27
+Delta5-65	206406	300	301	206406	300	301	300394	125935	174459	66636	37242	29394	0	1	110	0	152836	276	295	152836	214	219	32464	152836	19250	468	347	10	24479	16.02
+WT2-56	286047	300	301	286047	300	301	417406	176232	241174	94027	52040	41987	0	4	199	0	210367	274	294	210367	209	214	50835	210367	34541	641	495	25	36341	17.28
+Delta-Compl-m13	411102	300	301	411102	300	301	593586	249525	344061	140111	77498	62613	0	6	252	0	298688	273	294	298688	211	216	52642	298688	32333	763	635	30	42022	14.07
+WT2-38	149166	300	301	149166	300	301	217206	94928	122278	54791	29386	25405	0	2	86	0	105704	273	294	105704	208	213	24481	105704	16504	329	245	13	16957	16.04
+WT4-40	168601	300	301	168601	300	301	254714	112403	142311	54100	29753	24347	0	2	106	0	124970	274	293	124970	218	223	32342	124970	19370	437	313	4	23847	19.08
+WT5-41	204241	300	301	204241	300	301	299905	127886	172019	65883	36045	29838	0	5	131	0	151275	275	294	151275	213	217	33393	151275	21349	436	335	19	23720	15.68
+WT5-59	110399	300	301	110399	300	301	161367	68585	92782	36879	20400	16479	0	2	67	0	80888	275	294	80888	211	215	18050	80888	11695	234	175	4	12663	15.65
+WT3-39	426714	300	301	426714	300	301	646171	286374	359797	134714	72659	62055	0	5	273	0	317913	276	295	317913	217	222	66918	317913	42471	908	675	5	49513	15.57
+Delta1-61	150685	300	301	150685	300	301	220462	94303	126159	49686	26619	23067	0	2	70	0	111206	275	293	111206	212	216	29193	111206	18580	353	248	8	19507	17.54
+Delta-Compl-m17	293679	300	301	293679	300	301	423938	178372	245566	100063	55032	45031	2	4	175	0	213390	274	294	213390	211	215	48609	213390	29631	658	488	17	36785	17.24
+Delta-Compl3-69	308175	300	301	308175	300	301	453279	194094	259185	101330	55759	45571	0	7	187	0	226863	275	294	226863	212	216	48981	226863	31543	672	485	19	34443	15.18
+Delta-m8	357725	300	301	357725	300	301	517131	220008	297123	125402	68211	57191	0	3	180	0	257780	274	294	257780	209	214	58025	257780	36015	768	593	24	44004	17.07
+Delta-Compl3-51	224372	300	301	224372	300	301	338692	149956	188736	71554	38352	33202	0	4	158	0	166502	276	294	166502	214	217	36884	166502	23754	469	377	5	28536	17.14
+WT-m5	289245	300	301	289245	300	301	423686	182534	241152	98841	53785	45056	0	1	179	0	209669	273	293	209669	210	214	50982	209669	31365	709	534	23	37473	17.87
+Delta-Compl5-53	237864	300	301	237864	300	301	345033	146824	198209	81600	44476	37124	0	1	133	0	172685	274	294	172685	211	216	43603	172685	25331	583	494	30	35855	20.76
+Delta-Compl-m16	288015	300	301	288015	300	301	419243	181557	237686	103737	56050	47687	0	2	147	0	205432	272	292	205432	210	215	46850	205432	29332	618	467	13	32315	15.73
+Delta3-63	222072	300	301	222072	300	301	326450	139590	186860	72059	39360	32699	0	3	135	0	164258	276	294	164258	212	216	35082	164258	21830	460	313	7	25479	15.51
+Delta2-62	164442	300	301	164442	300	301	242339	102632	139707	51963	28810	23153	0	0	81	0	122402	275	294	122402	212	216	26257	122402	16825	363	268	7	18130	14.81
+Delta-Compl-m15	418436	300	300	418436	300	301	609183	256037	353146	136278	75936	60342	0	3	255	0	308899	276	295	308899	215	220	60440	308899	35027	811	613	5	47082	15.24
+Delta-Compl4-70	107928	300	301	107928	300	301	156568	67392	89176	39155	21383	17772	0	3	78	0	76922	273	294	76922	206	212	16613	76922	11364	174	140	10	11299	14.69
+WT-m3	200504	300	301	200504	300	301	292608	125811	166797	69132	37775	31357	0	4	140	0	145400	274	293	145400	213	218	37222	145400	21117	573	433	13	28638	19.7
+Delta-m9	387761	300	301	387761	300	301	565080	239350	325730	128635	71108	57527	0	2	253	0	284571	275	294	284571	215	220	58559	284571	32964	859	699	9	48851	17.17
+WT-m4	230052	300	301	230052	300	301	335061	142590	192471	77842	42667	35175	0	3	140	0	167547	273	293	167547	213	217	40772	167547	23115	582	462	14	32119	19.17
+Delta1-43	111119	300	301	111119	300	301	164940	71319	93621	34819	18704	16115	1	1	65	0	83251	277	295	83251	215	220	21736	83251	12491	317	253	7	17020	20.44
+Delta5-47	105780	300	301	105780	300	301	157377	68178	89199	33588	18311	15277	0	4	65	0	78600	275	294	78600	213	216	20546	78600	12155	261	196	10	15873	20.19
+WT-m2	242914	300	301	242914	300	301	361823	156379	205444	76300	41634	34666	0	3	160	0	181775	276	294	181775	217	222	50961	181775	30056	665	491	15	38556	21.21
+Delta-Compl1-49	170821	300	301	170821	300	301	247551	105837	141714	59032	31731	27301	0	0	109	0	123723	274	294	123723	210	215	32198	123723	20453	429	322	22	23107	18.68
+Delta-m11	531205	300	301	531205	300	301	776271	332807	443464	179648	97377	82271	3	7	342	0	387405	273	293	387405	210	214	79758	387405	52846	1013	749	32	54655	14.11
+Delta-Compl1-67	161052	300	301	161052	300	301	233910	100272	133638	56175	30391	25784	0	1	116	0	116422	275	294	116422	210	214	28502	116422	17937	358	269	13	20844	17.9
+Delta2-44	206706	300	301	206706	300	301	296977	128605	168372	76640	41011	35629	10	2	131	0	146356	273	294	146356	214	219	37769	146356	21196	571	421	14	28951	19.78

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/file30a47fca2dc3/shaman_greengenes_annotation.tsv → www/masque/done/filea1a9748bebd0/shaman_greengenes_annotation.tsv

 OTU	Kingdom	Phylum	Class	Order	Family	Genus	Specie
 OTU_15	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
-OTU_58	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae		
-OTU_36	Bacteria	Cyanobacteria	4C0d-2	MLE1-12			
+OTU_45	Bacteria	Cyanobacteria	4C0d-2	MLE1-12			
+OTU_14	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae		
 OTU_4	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
-OTU_23	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
-OTU_14	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae		
-OTU_12	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+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_26	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
-OTU_33	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
-OTU_62	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
-OTU_49	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae		
-OTU_44	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
-OTU_60	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
-OTU_13	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	enterica
-OTU_55	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
-OTU_21	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
-OTU_43	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	S24-7		
-OTU_25	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	aureus
-OTU_6	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
-OTU_41	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae		
+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_19	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium	acnes
-OTU_37	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae		
-OTU_22	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	
-OTU_42	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	
-OTU_57	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	enterica
-OTU_45	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	
+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_38	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
-OTU_34	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+OTU_47	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
 OTU_8	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	
-OTU_39	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	aureus
-OTU_61	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	aureus
-OTU_5	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	enterica
-OTU_31	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Salmonella	enterica
-OTU_32	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae		
+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_54	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_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_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);

www/masque/done/fileeec74b27d162.json

+{"type": "16S", "phredthres": 20, "annotationstrand": "both", "aFmax": 0.945, "aPmin": 0.75, "aSmin": 0.98, "path": "/tmp/RtmpSP5L8X/Masque_files", "aCmin": 0.785, "minreadlength": 50, "mail": "amine.ghozlane@pasteur.fr", "clusteringthreshold": 0.97, "aOmax": 0.865, "host": "", "name": "fileeec74b27d162", "aPmax": 0.785, "clusteringstrand": "both", "minampliconlength": 50, "dreptype": "--derep_prefix", "maxampliconlength": 0, "data_history_name": "data_shaman_2186_78", "aOmin": 0.82, "aGmin": 0.945, "aKmin": 0.75, "aFmin": 0.865, "paired": false, "result_history_name": "shaman_2186_78", "mincorrect": 80, "minabundance": 4, "contaminant": "/tmp/RtmpSP5L8X/fileeec74b27d162_contaminant.fasta", "aGmax": 0.98, "aCmax": 0.82}
\ No newline at end of file

www/masque/done/fileeec74b27d162/shaman_process_annotation.tsv

+Type	Count	Mean_length	Median_length
+Amplicon	197935	354	391
+Dereplication	76839	357	390
+Singleton_removed	4357	372	404
+Chimera_removed	3539	367	403
+OTU	290	325	404
+silva_annotation	289
+greengenes_annotation	289
+rdp_annotation	286