A newbie to QIIME2 here!
I am using phyloseq to analyze my 16S data. I created a BIOM file for analysis in R, when I am trying to create a phyloseq object I keep getting an error in R.
Is there something wrong with my BIOM file maybe? or the tree.object? I would appreciate your kind assistance.
I have attached my BIOM file and metadata
####Here is the script I ran in R
Load the biom files
file = “C:/Users/enghalipo/OneDrive - Namibia University of Science and Technology/Documents/PhD work/Data Analysis/16S/16S_taxonomy.biom”
Load the abundace tables
abundance.table = import_biom(file, taxaPrefix=F)
Load the mapping files
map = “C:/Users/enghalipo/OneDrive - Namibia University of Science and Technology/Documents/PhD work/Data Analysis/16S/metadata3.txt”
Load the mapping tables
mapping.table=sample_data(read.table(map, header=T, sep="\t", row.names=1))
#Create the Phyloseq objects
physeq=phyloseq(otu_table(abundance.table),tax_table(abundance.table), mapping.table)
physeq=subset_samples(physeq, Groups %in% c(“Hummock_10”,“Hummock_8”,“Hummock_5”,“Hummock_4”,“Hummock_2”))
#Quality Control
nsamples(abundance.table)
nsamples(mapping.table)
nsamples(physeq)
#Give a colnames to separate different taxonomic levels
colnames(tax_table(physeq))=c(“Domain”, “Phylum”, “Class”, “Order”, “Family”, “Genus”, “OTU”)
Load the tree file (use the unannotated.tree)
treefile = “C:/Users/enghalipo/OneDrive - Namibia University of Science and Technology/Documents/PhD work/Data Analysis/16S/97_otus_unannotated.tree”
tree.obj = import_qiime(treefilename = treefile)
Now merge the three separate phyloseq objects into a single object
otu.table = merge_phyloseq(physeq, mapping.table, tree.obj)
rownames(sample_data(otu.table))
colnames(sample_data(otu.table))
####Here is the error I am getting after the last command:
Error in validObject(.Object) : invalid class “phyloseq” object:
Component taxa/OTU names do not match.
Taxa indices are critical to analysis.
Try taxa_names()
16S_taxonomy.biom (3.7 MB) metadata3.txt (3.0 KB)
###The Qiime2 version I am using in our server
Python version: 3.6.7
QIIME 2 release: 2019.7
QIIME 2 version: 2019.7.0
q2cli version: 2019.7.0
