Hello,
I am running PICRUSt2 (version 2.5.2) on a set of ~130 samples with over 2,000 amplicons in total. I have run each individual step separately rather than using the entire pipeline at once. I have also provided local files to run it with my own sequenced genomes (i.e. 16S sequences for the tree, KOs, ECs for the metagenome prediction, 16S copy number, etc.). I ran it so I would generate the KO, EC, and metacyc predicted pathways. I also ran it so it would predict the contribution of each ASV per sample for each specific pathway.
This generated huge files with over 2,000,000 rows for the MetaCyc predicted profile (which it seems to be normal). However, when I look at a specific pathways (i.e. PWY-7198) that I know is present in the path_abun_unstrat.tsv file, some of them are not present in the path_cov_contrib.tsv or in the path_abun_predictions.tsv
Please see the screenshots below showing my grep results, as well as my unstrat file. I tried uploading the pred_cov_unstrat
Thanks in advance for your time and help,
Daniel.
path_abun_unstrat.tsv (766.4 KB)