importing ITS fungal data with qiime2R

Hello!
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):

in R:
physeqITS<-qza_to_phyloseq(
features=“q2files/ITS/table.qza”,
“q2files/ITS/taxonomy.qza”,
metadata = “q2files/metadata_R.tsv”
)
physeqITS
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).
THANKS!

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:

physeqITS<-qza_to_phyloseq(
     features=“q2files/ITS/table.qza”, 
     taxonomy=“q2files/ITS/taxonomy.qza”,
     metadata = “q2files/metadata_R.tsv”
)
3 Likes

Ohh indeed!! It works. Thanks a lot for this super fast and useful help!! greeting from Spain (night here)
Cheers!

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