Unable to successfully run codes in qiime2R

Hello,
I tried running these codes using the recently installed package “qiime2R”
dir.create(“testfolder”)
physeq<-qza_to_phyloseq(“table.qza”,“rooted-tree”,“taxonomy.qza”,“sample-metadata.txt”,tmp=“testfolder”)

These are the errors I got below
Error in unzip(file, exdir = tmp, list = TRUE) :
zip file ‘table.qza’ cannot be opened
In addition: Warning message:
In unzip(file, exdir = tmp) : error 1 in extracting from zip file

I have tried using all the suggestions from qiime2 forum and github but nothing is working. I am currently using windows 10 and R version 3.6.1.

Thanks,

Adesuwa

This would suggest that there is no file called table.qza in your working directory. Try typing list.files() and make sure that the file is present. you can change your working directory using setwd() or see which directory you are currently in using getwd() If not, you can always provide an absolute path like “/path/to/your/file/table.qza”.

1 Like

Hello, Adesuwa and Jordan!
Did you solve this problem in result?
I have the same!
To Jordan: all my files in one directory:
setwd("/home/ubi/tree")
And than I did:
physeq <- qza_to_phyloseq(
features = “table.qza”,
tree= “rooted-tree.qza”,
taxonomy= ‘taxonomy-sklearn.qza’,
metadata = “metadata1.tsv”
)

And result is absent:
Error in unzip(file, exdir = tmp, list = TRUE) :
zip file ‘taxonomy-sklearn.qza’ cannot be opened
In addition: Warning message:
In unzip(file, exdir = tmp) : error 1 in extracting from zip file

taxonomy-sklearn.qza - is after
qiime feature-classifier classify-sklearn
–i-classifier ./qza/taxa-naive-bayes.qza
–i-reads ./qza/sequences.qza
–o-classification ./qza/taxonomy-sklearn.qza

Please, help me to figure it out!

is it possible that taxonomy-sklearn.qza is in a subdirectory called qza? Try using list.files() to see what is in the current working directory. That error message comes from unzip but typically means it can’t find the file. I have added an extra line to provide a more informative error message and am pushing it to github now.

1 Like

Yes. taxonomy-sklearn.qza wasn’t is list.files()
Thank you!