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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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The same ASV is coming up in BLAST as a different taxonomy in comparison to when I run qiime feature-classifier classify-sklearn #2048

Closed ankurnaqib closed 3 weeks ago

ankurnaqib commented 3 weeks ago

I ran the whole qiime pipeline and I am seeing an issue here, and I am not sure why this is happening. For example, lets take ASVID e4326e04a50bad416b5aa32620852cbd (BLAST result)

But when I run the command qiime feature-classifier classify-sklearn \ --i-classifier /home/anaqib/References/qiime2_2023_5/silva-138-99-nb-classifier.qza \ --i-reads dada2-ccs_rep_filtered_v1.qza \ --o-classification dada2-ccs_classified_filtered_v1.qza \ --verbose \ &> DADA2_classifier.log

The output for the same ASV comes as:- <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

Feature ID | Taxon | Confidence -- | -- | -- e4326e04a50bad416b5aa32620852cbd | d__Archaea; p__Aenigmarchaeota; c__Deep_Sea_Euryarchaeotic_Group(DSEG); o__Deep_Sea_Euryarchaeotic_Group(DSEG); f__Deep_Sea_Euryarchaeotic_Group(DSEG); g__Deep_Sea_Euryarchaeotic_Group(DSEG); s__uncultured_archaeon | 0.712582

Any clue why this is happening? Any hekp would be really appreciated. Thank you.

benjjneb commented 3 weeks ago

This questinon is more suited to the Q2 forum. We do not implement the classify-sklearn method that you are using.

ankurnaqib commented 3 weeks ago

Thank you. Will do that.