Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/89210853ee884f1669710f868c6b9f/NTC_0001_0001_23H5VFLT4_s15.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/6f2df59a86526bb4010cd668be1efc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/9055d4b0da3d2fb2a1c6cf662c7616/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/6f2df59a86526bb4010cd668be1efc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0caad1614725c4cce40a4864004506/NTC_0001_0001_23H5VFLT4_s15.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

Get exon regions from ref_annot.bed ...
Load BAM file ...  Done
Total read pairs  used 4095