Windowmasker

# 2) Stage 2: apply those counts to produce interval masks
windowmasker \
  -ustat genome.counts \
  -in genome.fa \
  -out genome.mask.interval \
  -outfmt interval

# 3) Produce masked FASTA and combine with DUST
windowmasker \
  -ustat genome.counts \
  -in genome.fa \
  -out genome.masked.fa \
  -outfmt fasta \
  -dust true

Recommended Workflow

1. Run -mk_counts first on representative input to generate unit-count statistics.
2. Reuse the resulting counts file with -ustat during the masking stage.
3. Choose -outfmt based on downstream expectations, keeping in mind the default is interval output.
4. Tune memory and threshold parameters only after seeing default behavior on real data.

Guardrails

• -mk_counts and masking-stage options are separate modes; many arguments are mutually exclusive across them.
• -convert is for converting count-file formats, not for performing the normal masking stage.
• The default masking output format is interval, not FASTA.
• -mem applies to count generation, while -smem targets the size of the generated counts file.
• Repeat masking quality depends on representative counts; do not blindly reuse a counts file from a very different genome.