qiime2R support requests

[bsen2018]

Hi @jbisanz !

I installed tidyverse and qiime2R in my laptop (Windows10) which went through successfully. However, when I attempt to import the .qza files into R console I get the following error:

taxonomy<–read_qza(“taxonomy-blast.qza”)
Error in unzip(file, exdir = tmp) : ‘exdir’ does not exist

SVs<-read_qza(“table-no-eukaryote.qza”)
Error in unzip(file, exdir = tmp) : ‘exdir’ does not exist

Please help me out from this error. Thanks!

[shontie]

@jbisanz

The phyloseq() function is used to build a phyloseq object as per the explaination here. To create a ~standard phyloseq object you can use the qza_to_phyloseq() function as below:

Phylogenetic tree with 759 tips and 757 internal nodes.

Tip labels:

e9d3af4175420ffab49c29d1a6bb2030, 1830c14ead81ad012f1db0e12f8ab6a4, ca08eabd09756731f095632656d45b01, bfdc8d2e7693336b4f3781920d3fa253, 54a5af5112600a1faf06be268f95616e, 01173073677a287321be3484fbed0007, ...

Node labels:

root, , 0.765, 0.689, 0.455, 0.954, ...

[jbisanz (Jordan Bisanz)]

The function is trying to unzip the artifact to /tmp; however this may not be available on your windows system. You can specify a directory using the tmp="yourdirhere" argument. Something like this would work:

dir.create("scratch") #create a new folder in your working directory called scratch
tax<-read_qza("taxonomy-blast.qza", tmp="scratch")

[bsen2018]

This worked, but a new error pops up, here it is:

Any solution to this error? Thanks!

[jbisanz (Jordan Bisanz)]

Ahh, the issue lies in the sep="; ". This code assumed that your taxonomy string would have a space following the semicolon. if you switch to sep=";" I think it should work.