Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0352010e5727c976f7d16ce88a08da/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/28e55c7d2d3be7bf1f53282eb03b09/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/ab1ecef568cb5d38abb03fb63db551/aih-tih-sc-12b72b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/28e55c7d2d3be7bf1f53282eb03b09/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/46181f50f5c9d22d603ae1efa90e3e/aih-tih-sc-12b72b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-12b72b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000