Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/99e4235681285017e881cd944b496e/chip_pon.chip_pon.harmonized.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5a1f003e588603f457086de7e7a86c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5a1f003e588603f457086de7e7a86c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/2bbcc4e93222e2e85af74735d7bf7d/HCC1395_BL.GERMLINE.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/99e4235681285017e881cd944b496e/chip_pon.chip_pon.harmonized.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/2bbcc4e93222e2e85af74735d7bf7d/HCC1395_BL.GERMLINE.merged.vcf.gz
==> STAGING COMPLETE (6 inputs)

[INFO] Reading target VCF: HCC1395_BL.GERMLINE.merged.vcf.gz
[INFO] Reading source VCF: chip_pon.chip_pon.harmonized.vcf.gz
[INFO] Adding header fields with prefix 'CHIP_PON' for: FRACTION
[INFO] Building source variant lookup...
[INFO] Found 365410 variants in source VCF
[INFO] Processing target variants and merging characteristics...
[INFO] Complete! Processed 254 variants, matched 196 (77.2%)
[SUCCESS] VCF merging completed successfully!