Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/70ea73390d494f815dab3a1fc5117d/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  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/48/ffc9b8e7f403a33921ec33015e023f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/ffc9b8e7f403a33921ec33015e023f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/5bf1f747d4063c4602e14db4154f4b/aih-tih-sc-3abdf4-R1_A23YTGFLT4_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-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000