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/47/542ebcbc0f54fd8b27fe8772032e05/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/542ebcbc0f54fd8b27fe8772032e05/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/e963f580a4992dca43ab693e7c6488/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/dae1d6aa7b1426d476226fd533566f/aih-tih-sc-0754d2-R1_A23YTGFLT4_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-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000