feature-classifier fit-classifier-naive-bayes optimisation

[Nicholas_Bokulich]

Welcome to the forum, @jasongallant,
Thanks for digging up this old topic... some of the info I wrote in there a year ago is impacted by recent updates.

@jasongallant

qiime feature-classifier fit-classifier-naive-bayes is essentially silent about progress when working on the MIDORI reference, so its hard to say its “progressing”. Did you observe this?

That is correct — fit-classifier-naive-bayes does not give any "progress update" unfortunately.

@jasongallant

-Did you have any hints or scripts to facilitate this?

I'd recommend reducing database size to reduce runtime, if possible:

1. use extract-reads to focus on the amplicon region you are using
2. remove any low-quality sequences
3. dereplicate the database (ideally after extracting amplicons) to reduce database size and redundancy. You can use RESCRIPt to dereplicate the sequences together with the taxonomy.

@jasongallant

• -Did you ever succeed with BOLD? Any hints or scripts to help with loading this into qiime2?

RESCRIPt also has a "get-ncbi-data" method that you can use to download data from genbank and automatically format it and import it as QIIME 2 artifacts. Since BOLD deposits their public data on genbank (all or most? not sure), it would be possible to use that to grab public BOLD data.

Good luck!