Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/0a96b55d84d45d8460e84d472820bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/40d6ea0ee1da3f6e6ab38333b2b818/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/40d6ea0ee1da3f6e6ab38333b2b818/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/55ba7cb76d62f563f9e9f01f19fdf8/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/7ba4a71cca83f6facee8a0767ba77f/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000