problem with taxa summary (getting to many k__Bacteria)

Hi @Javad32,

The resolution of the screen-shots is a bit low and I am unable to read the output. But I assume some are Eukaryota? I would sanity-check this by classifying against the SILVA 138 reference sequences, as this is a larger reference set that also includes eukaryotes. The classifiers, and the files used to make them are located here.

If you are interested in making your own SILVA reference files, consider making use of RESCRIPt.

-Best
-Mike