Strange results identified based on taxa-bar-plots.qzv. Classifier problem?

Based on taxa-bar-plots.qzv I see that I am having many taxonomic classified up to only domain level (see the graph below). This is something unexpected for me. I thought that it has to do something with the classifier but while reading the QIIME2 forum it looks like I did everything correct (see the scripts below). Do you know what might be the reason it?


qiime tools import
--type 'FeatureData[Sequence]'
--input-path SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fna
--output-path SILVA_132.qza

qiime tools import
--type 'FeatureData[Taxonomy]'
--input-format HeaderlessTSVTaxonomyFormat
--input-path SILVA_132_QIIME_release/taxonomy/16S_only/99/taxonomy_7_levels.txt
--output-path SILVA_132_ref-taxonomy.qza
qiime feature-classifier extract-reads
--i-sequences SILVA_132.qza
--o-reads ref-seqs.qza
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads ref-seqs.qza
--i-reference-taxonomy SILVA_132_ref-taxonomy.qza
--o-classifier classifier.qza

I am using QIIME2 2019.4 installed by miniconda.

I will appreciate any help and comments. Thanks!

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