[Sat Oct 10 12:19:16 PDT 2026] 9 samples: Pum1 Qui1 Qui2 Qui3 Qui4 Rio1 Rio2 Rio3 Rio4
[Sat Oct 10 12:25:23 PDT 2026] strand tags done
[main] Version: 1.10.2
[main] CMD: biscuit pileup -@ 32 -m 20 -o output/13-wgbs-hapa/13.7-snps/wgbs_snps.all.vcf data/13-wgbs-genome-hapa/Och_HapA_assembly.fa output/13-wgbs-hapa/13.7-snps/yd-bams/Pum1.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Qui1.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Qui2.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Qui3.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Qui4.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Rio1.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Rio2.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Rio3.yd.bam output/13-wgbs-hapa/13.7-snps/yd-bams/Rio4.yd.bam
[main] Real time: 880.763 sec; CPU: 26264.588 sec
[Sat Oct 10 12:44:18 PDT 2026] pileup done
[Sat Oct 10 12:51:44 PDT 2026] 1547146 SNPs (QUAL >= 20); 51536 at CpGs
file  calls  with_CpG_SNP  pct
[Sat Oct 10 12:51:44 PDT 2026] done