The bioBakery help forum

Humann3 does not recognize "relative abundance" in metaphlan profile file


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.

Best wishes,

Hello - Thank you for the detailed post. Would you (if you have not already) double check that you have the most recent version of HUMAnN v3 installed? If you do have the most recent version and you still see the error would you provide a small example input file that replicates the error that you are seeing.

Thank you,