Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/69553138798f83f8e80b390f11a8e4/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/3c8d62dc6d65d71fe07b3391a2e13d/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/01ae3c9b49c283014fc4fb36e5bf23/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/22c1c312a741a59ca8bd3cbc27edb6/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/01ae3c9b49c283014fc4fb36e5bf23/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000