taxonomy.tsv error

[DECARO (CARMEN)]

Hi , I am Carmen
I have a problem with QIIME2 and Silva with taxonomy classification. I write the command that I did
1)
qiime feature-classifier extract-reads
--i-sequences silva-138-99-seqs.qza
--p-f-primer CCTACGGGNGGCWGCAG
--p-r-primer GACTACHVGGGTATCTAATCC
--o-reads silva-138-99-V3V4.qza
--verbose

qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads silva-138-99-V3V4.qza
--i-reference-taxonomy silva-138-99-taxa.qza
--o-classifier silva-138-99-V3V4-classifier.qza

3)qiime feature-classifier classify-sklearn
--i-classifier silva-138-99-V3V4-classifier.qza
--i-reads rep-seqs.qza
--o-classification taxonomy_silva-138-99-nb.qza

4)qiime tools export
--input-path table.qza
--output-path ASV-table

5)qiime tools export
--input-path taxonomy_silva-138-99-nb.qza
--output-path taxonomy

After these commands my feature table contains 9142 rows (like is reported in table.qza and rep-seqs.qza , because I controllen in qiime.view) but my taxonomy.tsv reported only 777 rows. How can I solve the problem?

[SoilRotifer (Mike Robeson)]

Hi @DECARO,

This is expected behavior, as multiple features (i.e. sequence variants) can map to the same taxonomy. For more details see here:

Features associated with ASV

Let’s say you have a feature table that looks like this: SampleID feature1 feature2 feature3 s1 7 1 9 s2 3 6 2 s3 0 13 0 The accompanying sequences file would look like this: feature1 ACGTGATCGTAGCTGAC feature2 TTGTGATCCTGAAGCTG feature3 TGTGTGACGTAGCTGAC and if you attempt to classify those sequences you will get a FeatureData[Taxonomy] artifact that looks like this …

-Cheers!
-Mike