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. 
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