Classification filtering only virus/archaea sequences

[NINADCROCHA]

Hi,

I have downloaded the centrifuge correctly and I have all the taxonomy files, including bacteria, viruses, archaea, fungi, and mammalian. I have a prevalence of bacterial DNA in my samples, however, it is not showing in my final OTU table. For some reason, it is classifying only viruses, archaea and a few eukaryotic samples, as you can see in the feature table above. Any ideas of what might be causing this? Thank you! feature-table_opti1_old.txt

[sanderdebacker]

More information about the database and commands you are using would be needed to help with this issue.