Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/c74031e45ad4dac87aabf3ddba9fd8/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/3c8d62dc6d65d71fe07b3391a2e13d/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/3f3337508d75a53c81a8a0348f3562/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/3f3337508d75a53c81a8a0348f3562/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/24a36d1d9196a6fd1fbf135356a4be/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000