Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/db0390e137cf3062481f869034d2c8/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/b7895934eb1a5bd210663a639af769/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/b7895934eb1a5bd210663a639af769/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3522bf601c26992c2b67a12656ce68/aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d672a47a266010b96e49181ec6830a/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000