Filtering metagenome amplicon sequencing data

Question

[kocharovskayaj]

Hello! I process my metagenomic data with QIIME2 plugin deblur. Please tell me why in some of my samples a large number of readings are in groups unique-reads-missed-reference and reads-missed-reference? How to fix it? With taxonomic classification, the remaining sequences are identified as 2 organisms, although there should be a large variety. Thanks for your help!