Abnormal high percentage of unclassified bacteria

Qiime2 version: 2023.9 installed by conda
database use for classification. GTDB

Beginner here.
I am getting around 50% of unclassified bacteria (p__Bacteria;;;), and I am assuming it's a problem because that's not usually the case. I used dada2 for denoising

$qiime dada2 denoise-single
--i-demultiplexed-seqs mergedseqs-goodfmt.qza
--p-trunc-len 280
--p-trim-left 40
--o-table dada2-table-280-40.qza
--o-representative-sequences dada2-seqs-280-40.qza
--o-denoising-stats dada2-stats-280-40.qza
--p-n-threads 8

$qiime feature-classifier classify-sklearn
--i-classifier SILVA515806_138_99_classifier.qza
--i-reads dada2-seqs-280-40.qza
--o-classification class-seqs-280-40.qza
--p-n-jobs 8

$qiime taxa filter-table
--i-table dada2-table-280-40.qza
--i-taxonomy class-seqs-280-40.qza
--p-exclude mitochondria,chloroplast,unassigned
--o-filtered-table filt-class-table-280-40.qza

Could you please help me see where the problem is?
I apologize in advance for the missing info. first time posting. Please feel free to ask for any!
Thank you!

Hi @Abdelhady_Elshal, welcome to :qiime2: !

If you search the forum, you find that the most common reason for this issue, is that your reads are in mixed orientation. Here is at least one thread that should help get you started:


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