Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ef3d0dd42feb793def198e10684fbb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/ade13c1bd1d8a3b73bbc3b3f9a6440/germline_control_2.haplotyper.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ef3d0dd42feb793def198e10684fbb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3f8adfacf79bd853c15f1cbb46456a/germline_control_2.dv_rescue.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/ade13c1bd1d8a3b73bbc3b3f9a6440/germline_control_2.haplotyper.unfiltered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3f8adfacf79bd853c15f1cbb46456a/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