Hi @reymonera
As metaphlan is producing the output (even if it is UNKNOWN 100%) it means that the execution was performed correctly. This is not really an error but a report saying that after mapping all your reads, MetaPhlAn is not able to detect any microbial species in your sample. This does not mean that your sample does not contain any microorganism, but that with the current parameters, MetaPhlAn is not able to detect them. By default, MetaPhlAn needs to find 20% of the markers of a species to report the species is present in the sample. This is controlled by the stat_q parameter (Check this post Fungal signatures - #2 by aitor.blancomiguez). In samples with low microbial biomass, 20% can be too strict (I am not an expert on human milk microbiome, but I think this might be your case). Reducing the --stat_q parameter (maybe to 10%) might help.