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/0b/861bbddc60881d48bd8fd2c10b027b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/861bbddc60881d48bd8fd2c10b027b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/9974715b26386cbe22e03d563a248d/aih-tih-sc-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/e3f8fc649ff395e795586b9719e337/aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000