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/e8/81a82fe0fd1c5c02ec0888205af191/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/39477d52a2eed0d9bae00888a91138/aih-tih-sc-150e73-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/81a82fe0fd1c5c02ec0888205af191/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/6886a2a72352f5efe0ff4e29278a8a/aih-tih-sc-150e73-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-150e73-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000