problem in classification

[Anita_Chand]

Hi everyone,
I am using MiDAS database for my classification.
I used the following workflow:

To import ref sequence
qiime tools import
--type FeatureData[Sequence]
--input-path midas-ref.fasta
--output-path midas-ref.qza

Import the taxonomy file.
qiime tools import
--type FeatureData[Taxonomy]
--input-path midas-taxonomy.txt
--output-path midas-taxonomy.qza
--input-format HeaderlessTSVTaxonomyFormat

Train the classifier.
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads midas-ref.qza
--i-reference-taxonomy midas-taxonomy.qza
--o-classifier midas-classifier.qza

To classify my data
qiime feature-classifier classify-sklearn
--i-classifier midas-classifier.qza
--i-reads mydata.qza
--o-classification taxonomy-mydata.qza

But I got strange output, I am unable to figure out the problem.

note: qza file for my data is from shotgun metagenomic using Oxford nanopore. fastq files converted to fasta and then to qza.

I hope to get some suggestion

Thank you

[cherman2 (Chloe Herman)]

Hi @Anita_Chand,
I could see a couple of reasons that this would happen.
My first thought is that this is happening because you are trying to classify metagenomic reads using a 16s classifier!

I would checkout our classify-kraken2 command:

draft tutorial for shotgun metagenomics with QIIME 2

Hi all, Following on our announcement of the first alpha release of the QIIME 2 Shotgun Metagenomics Distribution, we are starting to develop some alpha (early draft) tutorials. At the moment, we're going to keep these on GitHub and link to specific documents that you can view there. Before too long, we'll be starting to build and host Jupyter Books that cover tutorials for the different QIIME 2 distributions that are available. So, here's a first iteration of a bring-your-own-data tutorial co…

Make sure that you are using our shotgun-metagenomic distro!
https://docs.qiime2.org/2024.5/install/native/#qiime-2-metagenome-distribution

Let me know if you have any questions!