Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/0243baf59143a09530ee8911e13e43/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/dbb2986de30bc0c8e031aa91b68ddf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/dbb2986de30bc0c8e031aa91b68ddf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/ce33ecda1d6940901f8feedba9fc08/659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/b058659fd33f79c88e18ace448dbfc/659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000