Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/a6b2f3ae80298c2fa5863959a0395f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/a6b2f3ae80298c2fa5863959a0395f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/18fe20dd395ab631b4f57a91fcdb12/659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/f73a0e22861201cc7c5cccf07ed1b4/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/366e253fa972ac1ca727bbadf75240/659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000