Possible to get kingdom for each read?

Microbial community profiling MetaPhlAn
1

Hey I was thinking of using MetaPhlA3 to find out which kingdom each pair of reads belong to. The purpose of doing this is to subset my dataset by removing eukaryotic, viral, and archaeal reads and hopefully get a better assembly by the remaining reads.
MetaPhlA3 is able to generate an intermediate file telling which unique marker each read is hitting to. Is there a way to use that file, reverse engineer it and tell the kingdom that marker belongs to?

Thanks

2

MetaPhlAn is not designed to assign taxonomy to all the reads in the metagenome, but it reports presence and relative abundance of the detectables species by mapping the metagenome to a set of marker genes, so the resulting alignment reports only the reads that are matching to a marker gene.