Q2-compatible Silva reference sequences 404 not found

[adamova (Anja Adamov)]

Hi there,
I am attempting to fetch the reference SILVA v4 sequences pre-formatted for usage with QIIME2 from the official webpage "Data resources — QIIME 2 2024.5.0 documentation". When I attempt to download the "https://data.qiime2.org/2024.5/common/silva-138-99-seqs-515-806.qza" file I get the error that the webpage is "404 not found".

Is this a known issue? Or am I looking in the wrong place?

Your help is much appreciated.

Best,
Anja

[SoilRotifer (Mike Robeson)]

Try pulling from here:

QIIME 2 Resources

-Mike

[adamova (Anja Adamov)]

hi @SoilRotifer, thanks for your quick reply. The link you provided only includes trained classifiers not the respective reference sequences, no?
best, Anja

[Mike_Stevenson]

Hi @adamova

Try this link Silva database 138

Hope that’s what you’re looking for!

[adamova (Anja Adamov)]

thanks, I am aware of this resources and also the option of fetching the sequences with RESCRIPt. my question was rather targeted towards the pre-formatted files on the Q2 Data Resources webpage.

[SoilRotifer (Mike Robeson)]

@adamova

The link you provided only includes trained classifiers not the respective reference sequences, no?

Oh gosh, you're right! Sorry about that!

It appears that the files are not included in the latest release... not sure why. You can download them from the prior release here Just be sure to click the "Show me content on this page". The files are identical, but you'll have to train the classifier for 2024.5 based on these input files.

I'd recommend simply using RESCRIPt as outlined here, if you'd like to minimize any of the curation that was performed. Depending on what you are doing, the curation that was applied might be too agresive.