fit-classifier-naives-bayes error


I'm trying to run 'qiime feature-classifier fit-classifier-naive-bayes' using a publicly available qiime2 .qza files to build a Phytoref database in qiime2 format.

This is where I get my .qza files from Oceanic_database/PhytoRef at master · ndu-invitae/Oceanic_database · GitHub

I've run the same command about an year ago with the same files in a previous version of qiime2 and had no problem. But now I'm unable to execute the command and qiime gives the below errors

version used: 2021.8
command used: qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads Phyto_16S_plastid_qiime2.qza --i-reference-taxonomy Phyto_16S_plastid_taxonomy.qza --o-classifier classifier_phytoref.qza

Error: There were some problems with the command:
(1/2) Invalid value for "--i-reference-reads": 'Phyto_16S_plastid_qiime2.qza'
is not a QIIME 2 Artifact (.qza)
(2/2) Invalid value for "--i-reference-taxonomy":
'Phyto_16S_plastid_taxonomy.qza' is not a QIIME 2 Artifact (.qza)

I ran this on an HPC system.

Any help is much appreciated

Many thanks

Hello Uth,

I took a quick look at those .qza files, and it turns out they were imported using Qiime2 2018.6.0. That's pretty old!

I wonder if you extract the .fna files from the .qza archives and then import them again using your new Qiime version, that would work better.

Let us know what you try next!

Thanks for your reply.

The qza files are publicly available ones. I really have no idea how to convert the original fna files in PhytoRef database to qza.

Anyways, I decided to make a blast database with maksblastdb and classify the sequences. It seems easier at the moment.

Thanks again for taking your time to reply.


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