qiime2-metagenome-2024.5 feature-classifier

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1

Hi everyone,
I am trying to train classifier with ref sequence file and taxonomy file but the command ending with the message 'killed'.
qiime tools import
--type FeatureData[Sequence]
--input-path ref_seq.fa
--output-path ref_seq.qza

qiime tools import
--type FeatureData[Taxonomy]
--input-path ref_tax.txt
--output-path ref_tax.qza
--input-format HeaderlessTSVTaxonomyFormat

(qiime2-metagenome-2024.5) student@AMR-DELL:~$ qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads ref_seq.qza
--i-reference-taxonomy ref_tax.qza
--o-classifier classifier.qza
Killed

I tried different chunk-size still get the same error. I have memory availabe is 13 Gb.

Thank you
Anita

2

Hello Anita,

Welcome to the forums! :qiime2:

This skl training step takes a lot of memory!
When I run fit-classifier-naive-bayes I need at least 50 GB.

Do you have a computer with more RAM or an institutional HPC resource?

3

Hi @colinbrislawn,
Thanks a lot!
Unfortunately, I don't have any of them now.
Are there any alternatives? :slight_smile:

4

Sure!

What amplicon region did you sequence?
(16S V4, 18S, ITS, etc.)

Some databases for these regions are listed here: Data resources — QIIME 2 2024.5.0 documentation

If you want to use the skl classifier, we have some ready to use pre-trained classifiers here:

1 Like
5

I did shotgun metagenomic sequencing and I need to train a classifier with the latest MiDAS database.

6

Thank you for telling me more!

In case you have not found it already, take a look at our untargeted metagenomics tutorial:
https://cap-lab.bio/q2-books/intro.html

My guess is that building this database will happen outside of Qiime2. Then you can import it:

1 Like
9

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