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/df/b6085a6495f7e89e6e289e2c0e4692/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/2d67d5a5a11e18f048fd3290f95e0f/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/49f7ff2cc5744acceef005b69706a7/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/b6085a6495f7e89e6e289e2c0e4692/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000