Hi, I am new to HUMAnN3 (and HUMAnN) in general. I have no problem installing it using conda. I compared the mapping of the demo fastq file before and after installing the complete ChocoPhlAn and UniRef90 databases. Surprisingly, the percent mapped reads only improved marginally from
Unaligned reads after nucleotide alignment: 88.3095238095 %
Unaligned reads after nucleotide alignment: 87.3714285714 %, for ChocoPhIAn, and
Unaligned reads after translated alignment: 83.6190476190 %
Unaligned reads after translated alignment: 80.3904761905 %, for UniRef90.
Is there a mistake? Or is it common that only 20% reads map for a typical stool sample? (I understand that this may be a limitation of the NCBI database/ annotation rather than the pipeline per se).