Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/c89b1e6b4c11ffe89a5fae40dd3b8f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/9548a8f39577602f4935cadc49e876/germline_control_2.haplotyper.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/c89b1e6b4c11ffe89a5fae40dd3b8f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/f98e50afc5ad5ab8c6f65b5c00612c/germline_control_2.dv_rescue.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/9548a8f39577602f4935cadc49e876/germline_control_2.haplotyper.unfiltered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/f98e50afc5ad5ab8c6f65b5c00612c/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