Assign taxonomy of ASVs after using DADA2 on qiime2

[hadeerismail22 (Hadeer Ismail)]

Hi,
I want to use silva classifier for my sequences:
qiime feature-classifier classify-sklearn
--i-reads representative_sequences.qza
--p-reads-per-batch 5000
--i-classifier silva-138-99-515-806-nb-classifier.qza
--verbose
--o-classification ./taxonomy_1.qza
i got the result as: killed
i dont know the reason
Could you please help me?

[SoilRotifer (Mike Robeson)]

Hi @hadeerismail22, without more details, I'll make the assumption that your computer may not have enough memory. If you search the forum you'll find many threads about this.

SILVA, and other large classifiers often require more 24 GB or more of RAM. I'd suggest drastically lowering the --p-reads-per-batch to less than 1000, as this normally helps to alleviate memory pressure. If that fails, you may need to run on another system with more memory, or try one of the other feature classifier options like classify-consensus-vsearch.

[hadeerismail22 (Hadeer Ismail)]

Thank you for your advice
I tried classify-consensus-vsearch and i got
(1/3) Invalid value for '--i-reference-reads': Expected an artifact of at
least type FeatureData[Sequence]. An artifact of type TaxonomicClassifier
was provided.
(2/3) Invalid value for '--i-reference-taxonomy': Expected an artifact of at
least type FeatureData[Taxonomy]. An artifact of type TaxonomicClassifier
was provided.

[SoilRotifer (Mike Robeson)]

Hi @hadeerismail22,

@hadeerismail22

(1/3) Invalid value for '--i-reference-reads':
...
(2/3) Invalid value for '--i-reference-taxonomy':
...
An artifact of type TaxonomicClassifier was provided.

As the error messages say, you are providing a classifier, and not the actual reference sequences or taxonomy. You can obtain the premade reference sequence and taxonomy files for SILVA here. You can use these for the BLAST and VSEARCH classifiers. Actually, these files are used to make the classifier, which itself is only used for feature-classifier classify-sklearn.

-Mike

[hadeerismail22 (Hadeer Ismail)]

Thank you so much, i followed your steps and it worked finally after 8 days on my laptop
i am so happy for that, so grateful for you
i just have a last question i got two files from this command, Classification.qza, and search_results.qza files, i only used classification.qza file
what about the search_results.qza file? should i use it too?

Thanks a lot

[SoilRotifer (Mike Robeson)]

@hadeerismail22

i followed your steps and it worked

Great!

@hadeerismail22

i only used classification.qza file
what about the search_results.qza file?

Typically you'd want to use the classification output.

[hadeerismail22 (Hadeer Ismail)]

Thank you so much for your help