step1: download metaphlan databases
wget http://cmprod1.cibio.unitn.it/databases/MetaPhlAn/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.tar
step2: uncompress metaphlan databases
tar -xvf mpa_v31_CHOCOPhlAn_201901.tar
step3: specific the metaphlan databases location
humann \
--input final/ff05623391_kneaddata.fastq \
--threads 12 \
--metaphlan-options "--bowtie2db /16SrRNA/metaphlan/" \
--nucleotide-database 16SrRNA/humann/chocophlan/ \
--protein-database 16SrRNA/humann/uniref/ \
--output Microbiota/humann/