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/6c/4c5329b1a379df3ee892721cc0b6a5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/4c5329b1a379df3ee892721cc0b6a5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/b55b988f0db827ef6281c559d1ba3f/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/894c376224ce4045805d906648f998/659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000