Error importing .qza files into R as a phyloseq object

[ekquaye]

Hi JBisanz,

I tried importing .qza files (feature table, metadata file, taxonomy file, and a tree file) as a phyloseq object using the qiime2R package (version ‘0.99.6’), but I keep getting an error in the form "Error in FUN(X[[i]], ...) : numbers of left and right parentheses in Newick string not equal".

However,

1. I am able to create the phyloseq object without the tree file using qiime2R (version ‘0.99.6’)
2. Also, I am able to create the phyloseq object (including the tree.qza file) using an older version of qiime2R ('0.99.34') on a less powerful PC of mine.

Could you please help me overcome this error?

[jbisanz]

Interesting, this wouldn't be coming from qiime2R per se, but rather from the read.tree function of the package ape. It looks like this ?bug? was fixed in ape so I would think installing the latest version should fix your issue.

[ekquaye]

Thank you for the response, jbisanz. I use the latest version of ape (version 5.5), but, unfortunately, the error still persists.

[neal-caffry19]

@ekquaye Hi ekquaye,

Have you solved your problem yet? I met the same problem as you, can you tell me how you solved it?