Building standard db using k2 wrapper doesn't create taxonomy folder

[almutwerner]

• Command used: KRAKEN2/k2 build --standard --db standard_db --threads 20

• Problem: Cannot find taxonomy subdirectory in database, aborts

• It's a fresh installation.

I checked the scripts for potential error sources. The function for build_standard_database has download_taxonomy(args) (line 3064) commented out, which contains also the command to create the taxonomy subdirectory. The next command that is called after library download, build_kraken2_db, only checks if the subdirectories are there and exits if they aren't.

• Workaround: Manually running k2 download-taxonomy --db standard_db and then k2 build --db standard_db (without --standard; otherwise it seems to attempt to re-download everything)

[ch4rr0]

Hello

I left the download_taxonomy function on line 3064 commented. Uncomment that line and it should work. I will push a fix for this today.