MetaPhlAn 4.1 virome module not identifying known viruses

Hi there,

I was very excited to use MetaPhlAn 4.1’s virome module when I saw it had been released! I am having some trouble with it, though. I have some sequence files where I’ve spiked in viral RNA in known concentrations, but am unable to recover that data when using --profile_vsc. Is there something that I’m doing wrong in the code below to get output files that show empty VSC files? I would be happy to provide you with the sample file via email should it be helpful. Would love to use this tool, provided I’m using it correctly. :slight_smile: Thanks for any help you can provide me with!

Sample Composition:
-Human Coronavirus NL63
-Human Coronavirus OC43
-Human Coronavirus 229E
-Influenza B Virus
-Influenza A Virus; H1N1
-Influenza A Virus; H3N2

1.25 uL of each virus were spiked into 5.5 uL of sterile nuclease-free water, along with 2 uL of Universal Human Reference RNA prior to library preparation/sequencing on an Illumina platform.

Sequence reads were trimmed of adapters and technical sequence, and the MetaPhlAn 4.1 commands below were used:
for i in $fastqs_dir/*_R1_paired.fastq do echo "MetaPhlAn-ing $i" name=basename $i | cut -f1 -d_ metaphlan $i,${i/_R1_paired.fastq/_R2_paired.fastq} --input_type fastq --nproc 14 --profile_vsc -s "${outdir}/sams/${name}.sam.bz2" --bowtie2out "${outdir}/bowtie2/${name}.bowtie2.bz2" -o "${outdir}/profiles/${name}_profiled.tsv" --vsc_out "${outdir}/vsc/${name}_vsc.txt" done