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/a0/af9921ea01292f72b5806b69131119/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/af9921ea01292f72b5806b69131119/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/7cd2061c1c16e215b06cb192370845/tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/da47d93bf4d914f2e2abc11162b7d0/tih_rna_sample_00115_23H5VFLT4_s35.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_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled