We have several sequencing projects using the EMP protocol for both 16SrRNA and ITS (fungi) amplicons. I am using qiime2R to import qiime2 artifacts into R with no troubles. However, unfortunately I have issues with ITS dataset, becuse apparently, qiime2R expects a tree (we dont use tress for ITS data):
metadata = “q2files/metadata_R.tsv”
Error in access(physeq, “phy_tree”, errorIfNULL) :
phy_tree slot is empty.
Is there a way to avoid the requirment of a tree to create a phyloseq object? any better alternative from qiime2 artifacts to R in this case? (we would like to analyze foth 16S and ITS datasets in the same way if possible).
It shouldn’t require a tree, I think the problem is that the order of arguments is: features, tree, taxonomy, metadata. In which case, I think it is trying to read your taxonomy as the phylogenetic tree. The following should work: