Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/1802f773101f279965a5057dc9b41c/659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/5b/0824ce17c12716dead160b4e1d7dd6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/0824ce17c12716dead160b4e1d7dd6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/31e4ce64f6d1ae3ad80c5e6631c367/659_bGW-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_bGW-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