I am trying to use metaphlan3 for taxonomic binning of the reads. I am running this command, metaphlan 01.sm_AZ1.fasta --input_type fasta > AZ1.txt, after the completion of the run, the organism abundance file is showing abundance of UNKNOWN -1 100.0 and is ending up. Please help me where I am getting it wrong.
AZ1.txt (218 Bytes)
Thanks for getting in touch. can you provide us more information about the reads you are trying to profile? As MetaPhlAn is reporting UNKNOWN -1 100.0, it means that is not able to find enough species- specific marker genes in your reads for the species available in the MetaPhlAn DB.