I have used the q2-picrust2 plugin using the following code:
qiime picrust2 full-pipeline --i-table sequence_variants.qza --i-seq rep-seqs.qza --output-dir q2-picrust2-output --p-threads 1 --p-hsp-method mp -p-max-nsti 2 --verbose
It worked perfectly, and I got an output folder containing three qza files: ec_metagenome.qza, ko_metagenome.qza, and pathway_abundance.qza. I now want to do downstream analysis using the ggpicrust2 R package. However, the instructions (README) specify to use a file called "picrust2_out/KO_metagenome_out/pred_metagenome_unstrat.tsv/pred_metagenome_unstrat.tsv" from the output. Where are these files located and how can I access them? I only have qza files. Do I need to run the analysis in individual steps vs. using full-pipeline? Do I need to use the standalone Picrust2 tool vs. the Qiime plugin? I tried to export the qza file to see the files in it but I couldn't find anything resembling pred_metagenome_unstrat.