open the .qza files generated by q2-PICRUSt2 in R

[Alice]

Dear Gavin,

I run picrust2 analyses using the PICRUSt2 QIIME2 plugin and following your tutorial. 

I obtained the 4 output files (ec_metagenome.qza, ko_metagenome.qza, pathway_abundance.qza, pathway_coverage.qza). 

I would like to open those files with R to do further analyses, in particular see the features table (EC, KO or pathway) per sample.

In order to do that, I tried to use the read_qza function from the qiime2R package (https://rdrr.io/github/jbisanz/qiime2R/man/read_qza.html). But I get the following error:

Error in read_biom(paste0(tmp, "/", artifact$uui, "/data/feature-table.biom")) :

Both attempts to read input file:

/var/folders/x6/clm4hj_54rjbhvlq56n652sh0000gn/T//RtmpeaKkxD/1fbcde60-ecb7-4736-9c2f-3701f55d6e80/data/feature-table.biom

either as JSON (BIOM-v1) or HDF5 (BIOM-v2).

Check file path, file name, file itself, then try again.

 

I also tried to convert the .qza file to .biom file using the qiime tools export function and then to open the .biom file with read_biom but I get a similar error. Could you indicate me how to open those .qza files in R?

Many thanks for your help.

A.

[Gavin Douglas]

Hi Alice,

I would recommend exporting the QZA files to BIOM files as you have done. What I usually do to use BIOM files in R is to first convert them to the legacy TSV format:

biom convert -i INFILE.biom -o OUTFILE.biom.tsv —to-tsv

You can then read this file into R with the standard read.table function (and you can use the options skip=1 and comment.char=“” to skip the extra starting line and read in the headerline properly).

Best,

Gavin 

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