Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/013786bf60e48795a82bf865049234/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/4c8ba7fc0a561ef1a9e720b5f30758/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/4c8ba7fc0a561ef1a9e720b5f30758/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/a9dcb2751cb968ecf99ffcc4fef571/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/a9d937bc1c6ec362de7939e3cc3670/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000