Thank you for developing these helpful tools! I am working with humann3 recently. I realised that current version of humann3 will not correctly read relative abundance results from metaphlan3 output profile file, when “estimated_number_of_reads_from_the_clade” is included in the profile. Instead, it will take the “coverage” column as “relative abundance” and do to downstream analysis. Therefore, it will ignore many species. I fixed this by reformat the profile file and get rid of the “estimated_number_of_reads_from_the_clade” column. I thought it would be helpful to post this issue here. Hope this can be fixed in the future version.