Download nt_core Kraken2/Bracken database

[lpeirson (Laura Peirson)]

I need to use the nt_core Kracken2 database available here: Index zone by BenLangmead but it is not an option. Can it be added to the plugin?

-Version of QIIME 2 you are running, and how it is installed:
qiime2-metagenome-2024.10
installed successfully with conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml

• What is the exact command or commands you ran?

qiime moshpit build-kraken-db
--p-collection core_nt
--o-kraken2-database ./acgmb/cache:kraken_core_nt
--o-bracken-database ./acgmb/cache:bracken_core_nt
--verbose

• What is the exact error message?

Plugin error from moshpit:

Parameter 'collection' received 'core_nt' as an argument, which is incompatible with parameter type: Str % Choices('viral', 'minusb', 'standard', 'standard8', 'standard16', 'pluspf', 'pluspf8', 'pluspf16', 'pluspfp', 'pluspfp8', 'pluspfp16', 'eupathdb', 'nt', 'greengenes', 'rdp', 'silva132', 'silva138')

See above for debug info.

[misialq (Michal Ziemski)]

Hey @lpeirson,

thanks for your question and welcome to the Forum! Yes, we can and will add support for that - you can track the progress of that issue here. In the meantime, if you want you could download all the database files from the link you provided and import them into a QIIME artifact "manually", just as you would any kind of data - this should let you use the other actions before we make that option available.

Let us know in case you have any other questions!

Cheers,
Michal