Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/1a5d251a226dfcbbaba9247e2a6db0/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/e07bafc934da696ea81357c0ac2cf5/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/0b847d74e5e3e07a748ad558672c66/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/0b847d74e5e3e07a748ad558672c66/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/4be880eb6bc2edc369423e8ed7f0cb/rna_s1221_S42.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000