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/fd/3b6323ed88109c4f4ab47fcd327391/aih-tih-sc-0183f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/69f721aa7e67a7e5b545097803db4d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/277466002b9b93a2ca30c233ed6620/aih-tih-sc-0183f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/69f721aa7e67a7e5b545097803db4d/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0183f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000