Missing FASTA file paths from bac120 and ar122 GTDB metadata

[dgolden96]

Hi there,

I've managed to replicate the Kraken2 database creation process with the toy dataset as described in the ReadMe file, but I've run into a snag doing the same using metadata from the GTDB. The metadata files at the following URL don't seem to contain the FASTA file paths necessary for running the pipeline: "https://data.gtdb.ecogenomic.org/releases/release202/202.0/". Would you happen to know of a workaround by which I can use one of the other fields in the metadata to get the necessary filepaths?

Thanks!

[nick-youngblut]

You have to add the fasta files yourself to the table. The file paths would be specific to the genomes that you have locally downloaded. See https://github.com/leylabmpi/Struo2#downloading-genomes