Tool name: MetaPhlAn v4.0.6
I want to establish the relationship between reads and abundance, so I used the hyperparameter --bowtie2out metagenome.bowtie2.bz2 to save the Bowtie2 results. Each line is an ID and UniRef90_R5B287|1__8|SGB2091. I assume SGB2091 corresponds to the species of the reads. However, after manually calculating, I found that it does not match the output of MetaPhlAn’s profiled_metagenome.txt. The main reason is that there are many elements of SGB group such as SGB_14546_group in the abundance result but not in Bowtie2 results.
I would greatly appreciate any suggestions you may have. How is the SGB group constructed?