2025-11-22 11:22:03,690 [INFO] Discovered 112 samples across 16 locations.
2025-11-22 11:22:03,706 [INFO] Coverage summary exists; skipping coverage calculation.
2025-11-22 11:22:03,712 [INFO] Variant calling outputs present; skipping mpileup/call.
2025-11-22 11:22:05,957 [INFO] generated new fontManager
2025-11-22 11:22:11,202 [INFO] Pipeline complete. Outputs written to /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize