Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/7e40f56165a19134e1aba9b60dab0b/GM24385_0001_RNA_0001_23H5VFLT4_s48.Aligned.sortedByCoord.out.bam.bai
  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/21/7acdbaa3f5478961ba601e5b5f8c6b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/7acdbaa3f5478961ba601e5b5f8c6b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/9d83ec513ae19da8f8dfe36ba5274b/GM24385_0001_RNA_0001_23H5VFLT4_s48.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s48.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000