SILVA 138.1 LSU reference HELP

I downloaded “SILVA_138.1_LSURef_NR99_30_06_20_opt.arb.gz” from the arb-silva website to use as the classifier for 18S protozoa data in qiime2 2019.10.

Code:
qiime feature-classifier classify-sklearn
–i-classifier SILVA_138.1_LSURef_NR99_30_06_20_opt.arb
–i-reads rep-seqs.qza
–o-classification taxonomy.qza

Output:
(1/1) Invalid value for “–i-classifier”:
‘SILVA_138.1_LSURef_NR99_30_06_20_opt.arb’ is not a QIIME 2 Artifact (.qza)

Is there some type of way to convert the classifier file from .arb to .gza? Or is there somewhere else I need to download the LSU reference from?

Thanks!

Hello Matthew,

Take a look at the Training Feature Classifiers tutorial :point_left:

If you can convert the .arb file to .fasta, or download a fasta file directly, you should be good to go!

Colin

Hi @matthewbur,

The arb file is not the correct file to use. That is for use within arb. As @colinbrislawn suggests you can download the fasta, and other files directly. For this, I’d highly recommend using RESCRIPt to download the files you need. Note: due to some recent changes, you may need :qiime2: version qiime2-2021.2.

You can follow the approach outlined in this thread:

-Cheers!
-Mike

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