Hey,
Thanks for releasing the MetaPhlAn 4.1. It will be a great improvement. However when I am trying to find the virus from this version, so i am not able to find it. However, with Metaphlan 3.0, I can find 5% of viruses in my sample.
I downloaded the database mpa_vJun23 using the Metaplan download option. Then I am trying to find the viruses through these commands.
metaphlan Gut_MG0182_S52_L001_R1_001.fastq.gz --input_type fastq -o profiled_metagenome_3.txt --nproc 12 --bowtie2db /mnt/d/metaphlan_4.1_db/ --add_viruses --mpa3 --profile_vsc --ignore_bacteria --ignore_archaea
metaphlan Gut_MG0182_S52_L001_R1_001.fastq.gz --input_type fastq -o profiled_metagenome_3.txt --nproc 12 --bowtie2db /mnt/d/metaphlan_db --add_viruses --mpa3 --profile_vsc --ignore_bacteria --ignore_archaea
metaphlan Gut_MG0182_S52_L001_R1_001.fastq.gz --input_type fastq -o profiled_metagenome.txt --profile_vsc --nproc 12 --bowtie2db /mnt/d/metaphlan_4.1_db/
I can successfully get the Archea and bacteria but cannot get the virus in the same fastq file where I am getting 5% viral reads from Metaphlan3.