MetaPhlAn3.0 virus profiling

Got no virus abundance with MetaPhlAn3.0 output. Can anyone please explain? My command is:
metaphlan xyz.fastq.gz --input_type fastq --nproc 8 > xyz.fastq_profile.txt

Thanks
DC7

By default, MetaPhlAn does not profiles viruses, you should run it with --add_viruses

1 Like