How virus abundance is calculated？

[AndAvia]

hi there，
You guys did a great job with the visualization part of the article and I've been reproducing it lately. But I don't know how the viral abundance files you provided (Figures 2 and 3 viral abundance matrix..txt) were obtained. I checked your code.
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  makeblastdb -in HQMQLQ.bins.fna -dbtype nucl -out HQMQLQdb
  blastn -query HQMQLQ.bins.fna -db HQMQLQdb -outfmt '6 std qlen slen' \
  -max_target_seqs 10000 -perc_identity 90 \
  -out virusxvirus.m6 -num_threads 40

  python /app/anicalc.py -i virusxvirus.m6 -o virusxvirus.ani.tsv
  python /app/aniclust.py --fna HQMQLQ.bins.fna --ani virusxvirus.ani.tsv --out virus.clusters --min_ani 95 --min_qcov 0 --min_tcov 85
  
  cut -f1 virus.clusters  > viralreps.txt
  seqtk subseq HQMQLQ.bins.fna viralreps.txt > viralreps.fna 

  ### Combine with MGVdb 
  pigz -fdc ${MGVdb} > mgvreps.fna

  #cat viralreps.fna mgvreps.fna > viruses.fna
  cat viralreps.fna > viruses.fna
  makeblastdb -in viruses.fna -dbtype nucl -out HQMQLQdbreps 

  ### Blast Genecatalogue against the viral references
  gunzip -fdc ${Genecatalogue} > MGX.genecat.fna

  blastn -task megablast -db HQMQLQdbreps -query MGX.genecat.fna -out HQMQLQ.genecat.m6 -outfmt 6 -num_threads 40 \
  -evalue 0.01 -qcov_hsp_perc 80 -perc_identity 90 -word_size 20 -reward 2 -penalty -3 -max_target_seqs 10 -max_hsps 1

`Question 1: I would like to know how to get the MGX.genecat.fna file inside?

Rscript --vanilla --slave Rscripts/get_viral_abundance_matrix.R HQMQLQ.genecat.m6 TPMmatrix.txt matrices

Question 2: I would like to know if the TPMmatrix.txt file for this R script input was obtained by directly quantifying the 5251 vOTUs with coverm, or was it obtained by some other method?

I would like to follow your quantitative approach to my own data，so your Q&A is very important to me, thank you most sincerely!