Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/06ef061c7b0f9e35e21bb93e492047/GM24385_0001_RNA_0001_23H5VFLT4_s32.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/2f/3eaff7665e576dd216e59564783c63/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/3eaff7665e576dd216e59564783c63/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/03cfc4207eb002aeb18f46e1cc3627/GM24385_0001_RNA_0001_23H5VFLT4_s32.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_s32.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000