Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/f45e698468353ec156d5f9b2359a98/chip_pon.chip_pon.harmonized.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/7b9ec744383961f9b212562dc7e91d/659_bTo-N1-BDNA-1_B23KFG5LT4_1.GERMLINE.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3ed18aa42c24a4118d6f76f1916bd5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/7b9ec744383961f9b212562dc7e91d/659_bTo-N1-BDNA-1_B23KFG5LT4_1.GERMLINE.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3ed18aa42c24a4118d6f76f1916bd5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/f45e698468353ec156d5f9b2359a98/chip_pon.chip_pon.harmonized.vcf.gz.tbi
==> STAGING COMPLETE (6 inputs)

[INFO] Reading target VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.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] Processed 10000 variants, matched 7390 with source...
[INFO] Processed 20000 variants, matched 15125 with source...
[INFO] Processed 30000 variants, matched 21534 with source...
[INFO] Complete! Processed 30934 variants, matched 22240 (71.9%)
[SUCCESS] VCF merging completed successfully!