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/dd/4cb30df4602a46b60ef0b062b8c0e0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/4cb30df4602a46b60ef0b062b8c0e0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/632bffbeed98a690b177578041a4ec/tih_rna_sample_00116_23H5VFLT4_s36.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/61abda3a3769f07c19974a889853e1/tih_rna_sample_00116_23H5VFLT4_s36.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_00116_23H5VFLT4_s36.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled