Unable to find all taxon as a result of taxanomic analysis

[HafizaHira]

I have paired-end sequencing reads of sample and I followed the same pipeline described in [“Moving Pictures” tutorial — QIIME 2 2024.10.1 documentation] for finding which bacterial species are present in which sample and I am getting two problems.
As I am giving 18 paired-end sequences as input. But as a result of denoising step, I am getting output as rep-seq.qza file that contains 40 sequence counts. I am confused isn't it too low ?
2: During the taxanomic analysis , it's only assigning the top level taxon like k-Bacteria. I am unable to find which bacterial species are present in which sample. Please guide me. I am attaching both files along with the post.
rep-seqs.qzv (206.0 KB)
taxonomy.qzv (1.2 MB)

[SoilRotifer (Mike Robeson)]

Hi @HafizaHira,

I've also tried classifiying your sequences, and even re-oriented them using qiime rescript orient ... and obtained poor taxonomic assignments. Even manual BLAST searching with megablast and ignoring uncultured/unclassified reads also return poor assignments. I think these are contaminant or off-target reads.