Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/98329a4dee105b807f073183444790/.command.sh
  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/e7/98329a4dee105b807f073183444790/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/df9810f41a37f074d5c9c86ba6f599/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0508594000c2359eddbe03f00fbe2d/659_bQZ-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_bQZ-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