Error in generating taxonomy

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I have used QIIME2 for my 16S metagenomic samples. I had some single end samples and some were paired end so I analyzed those separately and then combined the repseqs and tables generated by two analysis but now that I am trying to generate taxonomy there has been an error because most of the samples are not showing taxonomy after bacteria (kingdom level), while rest of the samples are only showing taxonomy against few genera and there are lots of unclassified sequences. I have used pre-trained classifier provided with the moving pictures tutorial. If I use a full length classifier will that solve my problem?. If not kindly guide me through this problem because I dont have the primer sequences used for my paired end reads to train my own classifier. (sequences was done by some other people and I dont have access with them now). I am attaching the repseqs and tables I want to use for analysis. Thanks a lot for your time.
Best regards,

Faizan Saleemmerged_rep-seqs.qza (264.4 KB)
merged_rep-seqs.qzv (759.2 KB)
merged_table.qza (331.8 KB)
merged_table.qzv (570.0 KB)

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Sounds like you are using the wrong classifier for at least one of these. Classification only to kingdom level is a very clear indicator of that. The full-length classifier should work fine for both as long as your amplicons are all 16S rRNA gene sequences, not need to know which primers you used.

Good luck!

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