Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/08673ee12ee6a0211e830547e14205/659_bCu-T1-TRNA-1_A23MVY2LT4_1.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/b0/3fed43af6c8cab09bac61aa8baeb32/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/3fed43af6c8cab09bac61aa8baeb32/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/4d11b394d48aa0fc84d79c8c8c6711/659_bCu-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000