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/95/daf5ff605b5373e058d70bb67b8eb8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/daf5ff605b5373e058d70bb67b8eb8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/eb1b4bc33e6f99dbd09d96c103560c/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/e87537765025c6c20022ca0a8a658b/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000