Qiime2 silva 16s v3v4 classifier test output odd


I have used silva 132 qiime release to learn training on 16s V3-V4 region ( I know there is a post in the forum provided the classifier but I am doing this for learning purpose).

Testing the classifier of silva 132 qiime release on 16s V3-V4 region yielded only Taxons belonging to Archae result.

which seems odd, I would expect bacteria taxons come out from it.

For input sequences, I used <rep set 16s only> at 99; for taxonomy, I used <16s only><99> consensus_taxonomy_7_levels.txt

printf "Import Sequence\n"
qiime tools import
--type 'FeatureData[Sequence]'
--input-path ../silva_132_99_16S.fna
--output-path silva_132_99_16S.qza

printf "Import taxonomy file\n"
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path ../consensus_taxonomy_7_levels.txt \
--output-path taxa_silva_ref_16s.qza

printf "Extract reference reads\n"
qiime feature-classifier extract-reads \
--i-sequences silva_132_99_16S.qza \
--p-trunc-len 500 \
--o-reads ref_silva_16s_99_seqs.qza

printf "Train the classifier\n"
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads ref_silva_16s_99_seqs.qza \
--i-reference-taxonomy taxa_silva_ref_16s.qza \
--o-classifier classifier_silva_16s_99.qza

qiime feature-classifier classify-sklearn \
--i-classifier classifier_silva_16s_99.qza \
--i-reads ref_silva_16s_99_seqs.qza \
--o-classification taxa_test_training.qza \
--n-jobs 1 \
--p-reads-per-batch 1000

qiime metadata tabulate \
--m-input-file taxa_test_training.qza \
--o-visualization taxa_test_training.qzv

I think I either used the wrong files or missed some steps?


HI @Xio_Lee,
See this post (and the rest of the thread) for a diagnosis and how to fix:

I hope that helps!

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