Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/b02a7396bf6caf366aae276126d7b9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/51797654e341f5a43c69a2d35fb1f1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/f198a43e0b3b36a809705502818a7f/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/51797654e341f5a43c69a2d35fb1f1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/4472770aae09656741932a093fa6a1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled