Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/6fd23e85f78a8fbdafb08660cd0e69/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d412b478254a8ff9fd9da7b4e3428c/germline_control_2.haplotyper.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/6fd23e85f78a8fbdafb08660cd0e69/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/65f3570d288d0fca8a7bb0d658e737/germline_control_2.dv_rescue.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d412b478254a8ff9fd9da7b4e3428c/germline_control_2.haplotyper.unfiltered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/65f3570d288d0fca8a7bb0d658e737/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