[Fri Oct  9 19:26:36 PDT 2026] 9 samples: Pum1 Qui1 Qui2 Qui3 Qui4 Rio1 Rio2 Rio3 Rio4
[Fri Oct  9 19:31:52 PDT 2026] strand tags done
[main] Version: 1.10.2
[main] CMD: biscuit pileup -@ 32 -m 20 -o output/13-wgbs/13.7-snps/wgbs_snps.all.vcf data/13-wgbs-genome/merged_out.fasta output/13-wgbs/13.7-snps/yd-bams/Pum1.yd.bam output/13-wgbs/13.7-snps/yd-bams/Qui1.yd.bam output/13-wgbs/13.7-snps/yd-bams/Qui2.yd.bam output/13-wgbs/13.7-snps/yd-bams/Qui3.yd.bam output/13-wgbs/13.7-snps/yd-bams/Qui4.yd.bam output/13-wgbs/13.7-snps/yd-bams/Rio1.yd.bam output/13-wgbs/13.7-snps/yd-bams/Rio2.yd.bam output/13-wgbs/13.7-snps/yd-bams/Rio3.yd.bam output/13-wgbs/13.7-snps/yd-bams/Rio4.yd.bam
[main] Real time: 553.708 sec; CPU: 16820.950 sec
[Fri Oct  9 19:47:09 PDT 2026] pileup done
[Fri Oct  9 19:53:45 PDT 2026] 952169 SNPs (QUAL >= 20); 31673 at CpGs
file            calls  with_CpG_SNP  pct
DML_Qui_vs_Rio  1314   6             0.5
DMR_Qui_vs_Rio  305    9             3.0
[Fri Oct  9 19:53:45 PDT 2026] done