Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/682e371175457d4a901ea58b836e9c/aih-tih-sc-318819-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/ce/435acbd5bccca6a8f0b85a1fe42038/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/0e830bcbe878e515254df17d01003a/aih-tih-sc-318819-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/435acbd5bccca6a8f0b85a1fe42038/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000