Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/308b93e5cf5c01971071b8a7062ad1/13511611-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/a838b73be236071d0f9aeb857c2181/D0000476_22q.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/0c5cdf793c58ead0acab0e1b24f430/SH032_HG513.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/1ef229200ddb745bd7736e90c57d10/5PercentHG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/3bbe2731b6bf51c4a55997e1f0dbd6/1_25PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/1510c66c876476137edc3bbdac1fd6/14668865-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/3f64319eb03f6f7f3827d9131a58fa/14862332-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/b28f73d5885260090f8b4337f88b81/15921737-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/cf94d9f5d6b7d25cbb61dfa9259f65/D0001109_22q.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/f039d684f79432d165706843c2d55c/SH032_HG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/e8eeeb284160770e03c71ea93113e7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2b9619ebfdec27cb35f6ca0c0ccdf5/13739430-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/be52efa25189ad9f5bbb1719f49cc5/14138939-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/97b488358c65bab57a0b8db38e5046/3140_NA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/b4ce9b62947c16a5cb7f31100f14f0/40PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/6d4c8374d4e70b8323f3e8773b6c20/3140_NA24143.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/b17ffec60065d37438a89abbc0fa25/20PercentHG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/965640018b08d16d35c8fffe5b5435/5PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/7464c340e302467f8be4d2ec8f5548/10PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/78d5607acce087ff10fb4da977ad17/13929215-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/f4f14496a62491c878f7a267d025f3/2_5PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/d62df0c0ed443628283361b62e62e7/20PercentNA24385.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/9f8586e76e39128ddcb2ec277ce029/13432478-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/35e20d75a0d72ff5ef5050f07c6e10/15451964-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/ca25918ff13845b91c30195f0d21e3/D0000162_22q.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/935484425a854c46aeff093a4badde/10PercentHG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/b216d4736fe58e99305ebeff846d29/16098090-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/a54c7ed766f3e67127cc63365715a4/1_25PercentHG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/10d2781727ae47228b888f95f4dac0/D0001483_22q.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/8e6f42987dfdcce53bdd89bca08f46/2_5PercentHG514.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/c9d6d05cbaf16d56398bc6dfbe2254/14558439-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/98ca624d8bb20a935c68c2391b639e/14389853-cfDNA.vaf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/e8eeeb284160770e03c71ea93113e7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/2b0a69ae94fc287d7f47aa5182563c/40PercentHG514.vaf
==> STAGING COMPLETE (34 inputs)

Warning: Sample 13432478-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 13929215-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 14138939-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 14389853-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 14558439-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 14668865-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 14862332-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample 16098090-cfDNA.vaf has no positions with depth > 0. Marking as insufficient_data.
Warning: Sample D0000162_22q.vaf has no positions with depth > 0. Marking as insufficient_data.

=========================================
SUMMARY: Samples with insufficient data
=========================================
Total samples with zero depth: 9
  - 13432478-cfDNA.vaf
  - 13929215-cfDNA.vaf
  - 14138939-cfDNA.vaf
  - 14389853-cfDNA.vaf
  - 14558439-cfDNA.vaf
  - 14668865-cfDNA.vaf
  - 14862332-cfDNA.vaf
  - 16098090-cfDNA.vaf
  - D0000162_22q.vaf

These samples are marked as 'insufficient_data' in output files.
=========================================