I am trying to upload my 3 seperate file (otu, tax and metadata), they all seem to be in the good format, but when I try and upload them, I get the generic error Troubleshooting
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I have tried it many times. I am working the with data, I got from an initial phyloseq object in R, that I converted to .csv files for putting them into microbiome analyst. Here are snippets of my 3 tables when opened in notepad++
OTU_table:
#NAME,BlankPCR,SensaGW06,SensaGW09,SensaGW10,SensaGW12,SensaGW13,SensaGW14,SensaGW16
otu0001,0,1303,18898,28896,101,858,0,346
otu0002,0,1275,7562,0,8903,0,17187,2495
otu0003,0,1051,52,16579,0,238,0,808
otu0004,0,204,646,0,82,1660,0,13896
otu0005,0,10773,243,508,4302,230,49,232
otu0006,0,549,98,0,490,2777,7512,4836
otu0007,0,10610,0,0,0,0,34,0
otu0008,8718,13,280,307,37,923,100,249
Tax_table:
taxonomy,Kingdom,Phylum,Class,Order,Family,Genus,Species
otu0001,Bacteria,Pseudomonadota,Gammaproteobacteria_2,Burkholderiales_2,Gallionellaceae_2,Gallionella_2,NA
otu0002,Bacteria,Campylobacterota,Campylobacteria,Campylobacterales,Sulfurimonadaceae,Sulfuricurvum,NA
otu0003,Bacteria,Pseudomonadota,Gammaproteobacteria_2,Burkholderiales_2,Comamonadaceae_2,NA,NA
otu0004,Bacteria,Pseudomonadota,Gammaproteobacteria_2,Burkholderiales_2,Gallionellaceae_2,Gallionella_2,NA
otu0005,Bacteria,Pseudomonadota,Gammaproteobacteria_2,Burkholderiales_2,Comamonadaceae_2,NA,NA
Metadata_table:
#NAME,Primerpairname,SampleID,Mibirem_name,Sample_or_Control,Order.Treatment,SUM_BTEX,Sum.PAH…16.EPA.,Naphthalene,X1.Methylnaphthalene,X2.Methylnaphthalene,Acenaphthylene,Acenaphthene,Fluorene,is_neg
BlankPCR,515fimp-806rimp,Blank,Blanc,Control Sample,1,0,0,0,0,0,0,0,0,TRUE
SensaGW06,515fimp-806rimp,SensaGW06,DE_KIE_01_GW,True Sample,2,22,0,0,0,0,0,0,0,FALSE
SensaGW09,515fimp-806rimp,SensaGW09,DE_KIE_02_GW,True Sample,3,0.5,15.4,1.1,0.11,0.06,1.4,12,0.65,FALSE
SensaGW10,515fimp-806rimp,SensaGW10,DE_KIE_03_GW,True Sample,4,1,17.4,1.5,0.07,0.05,1.2,14,0.67,FALSE
SensaGW12,515fimp-806rimp,SensaGW12,DE_KIE_04_GW,True Sample,5,16.8,97.3,22,6.9,11,1.1,48,22,FALSE
SensaGW13,515fimp-806rimp,SensaGW13,DE_KIE_05_GW,True Sample,6,228.8,600,120,40,4.5,2.5,390,73,FALSE
SensaGW14,515fimp-806rimp,SensaGW14,DE_KIE_06_GW,True Sample,7,1158.6,1270,72,510,380,48,500,360,FALSE
SensaGW16,515fimp-806rimp,SensaGW16,DE_KIE_07_GW,True Sample,8,0,20.2,0.71,0,0,0.16,19,0.052,FALSE
There was a formatting mistake in my metadata file, found it, thanks anyways.
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