Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/013786bf60e48795a82bf865049234/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/5132774ff718ed5b300ba31dcae048/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/5132774ff718ed5b300ba31dcae048/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/c3a872b13b04e87d8c489ba26c2dca/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/c9d89dceb8ea0fc52bb470c68ae975/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000