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/6e/eceb796414e8a424956676ba74f1b5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/eceb796414e8a424956676ba74f1b5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/65317c0d7e01654d97a67aea9d5671/tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/60cca2875f49132e8930798965d69a/tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000