Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/e88fd7fc7045f143707b3a331bf8bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/46366c8ffc7788a9dd4b53a5d32791/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/78880aa9d63347a65ceb8ec5a63b37/tih_rna_sample_00594_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/46366c8ffc7788a9dd4b53a5d32791/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/358042018d33530932b1c9d34313a0/tih_rna_sample_00594_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled