Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/9718430fe20a6a2af4bd92330716eb/659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  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/95/e7a1d259461fb6c350af39ee3c8f96/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/e7a1d259461fb6c350af39ee3c8f96/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/3aaf6df0c0e98be6b29aefdbd497da/659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_cIX-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