Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/47682aca1a1d5c539a8b9cd02483e8/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  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/33/eb15d6741eac07717efb55b363990d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/eb15d6741eac07717efb55b363990d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/86d6944c8bcf236ec9d71b3a03b96f/aih-tih-sc-1351d2-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-1351d2-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000