Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/aca3056163790b944a51a20dfe1a61/659_cRB-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/f1/0abdaac574582550d1bb9ccd88aafe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/a5715087dac937adba901ed7923e30/659_cRB-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/0abdaac574582550d1bb9ccd88aafe/.command.run
==> STAGING COMPLETE (5 inputs)

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