Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/65bae98ba25882414b5cb08766280a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/669017e9ebd9ea4d4591e2e870af75/germline_control_2.haplotyper.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/65bae98ba25882414b5cb08766280a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/b672e8bdcc343a6f653734dd3cebda/germline_control_2.dv_rescue.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/669017e9ebd9ea4d4591e2e870af75/germline_control_2.haplotyper.unfiltered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/b672e8bdcc343a6f653734dd3cebda/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