Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/cccf6b113e78dd73b3140b45d2ee6c/HCC1395_BL.chip.harmonized.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/2bbcc4e93222e2e85af74735d7bf7d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/2bbcc4e93222e2e85af74735d7bf7d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/cccf6b113e78dd73b3140b45d2ee6c/HCC1395_BL.chip.harmonized.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/60b0670bf396b776895de5560f968b/HCC1395_BL.germline.harmonized.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/60b0670bf396b776895de5560f968b/HCC1395_BL.germline.harmonized.vcf.gz.tbi
==> STAGING COMPLETE (6 inputs)

/tmp/nxf.92bOl1ICke/nextflow-bin/merge_vcf_characteristics.py:260: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
  return int(variant.format('DP')[sample_idx])
/tmp/nxf.92bOl1ICke/nextflow-bin/merge_vcf_characteristics.py:262: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
  return int(variant.format('GQ')[sample_idx])
[INFO] Reading target VCF: HCC1395_BL.chip.harmonized.vcf.gz
[INFO] Reading source VCF: HCC1395_BL.germline.harmonized.vcf.gz
[INFO] Adding header fields with prefix 'GERMLINE' for: GT, AD, DP, GQ, QD
[INFO] Building source variant lookup...
[INFO] Found 354 variants in source VCF
[INFO] Processing target variants and merging characteristics...
[INFO] Complete! Processed 254 variants, matched 41 (16.1%)
[SUCCESS] VCF merging completed successfully!