Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/e95737087e0e0da844d8437457d0bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/697e007474e45da2dea77ae0498539/germline_control_2.haplotyper.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/e95737087e0e0da844d8437457d0bf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b33ce4291edd44e519e78f21b01746/germline_control_2.dv_rescue.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/697e007474e45da2dea77ae0498539/germline_control_2.haplotyper.unfiltered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/b33ce4291edd44e519e78f21b01746/germline_control_2.dv_rescue.vcf.gz
==> STAGING COMPLETE (6 inputs)

INFO: Loading Sentieon variant positions...
INFO:   394 variant positions in Sentieon VCF
INFO: Scanning DeepVariant VCF for novel INDEL positions...
INFO:   0 PASS INDELs in DeepVariant VCF
INFO:   0 novel positions (not in Sentieon) -> written to germline_control_2.dv_only_sites.vcf.gz