Trying to run Humann3 on a set of MAGs

Microbial community profiling HUMAnN
1

Humann v3.9.

Hello all. Thanks for this amazing tool.
I have a question regarding the input files required by humann. I want to annotate pathways contained in my MAGs, but when I run humann, no species are selected from prescreen and no pathways are found. Only few hits in some MAGs. Gene families are found but with few hits (100kb at most). I have read in the documentation that input files for humann are intended to be reads from a metagenome, is that why I can’t get hits? I have also tried to map my MAGs to the curated reads so I get .sam files. This way I get no warnings or errors but the files are empty. This sam files are several gb, could this be the reason why it can not get hits?
I am using a 128gb ram workstation.

Thanks in advance
Carlos

2

HUMAnN is designed for analyzing unassembled shotgun metagenomes and metatranscriptomes (i.e. the original sequence reads). To annotate MAGs you would want to approach the problem more like genome annotation, e.g. with a workflow like Prokka.