Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/f46c446ee3afbc48176b612ea190de/aih-tih-sc-3270ab-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/a3/5384a3c1fa9f15a2e6e4bd11fcdbeb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/5384a3c1fa9f15a2e6e4bd11fcdbeb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/b41a656e5398795a74f124141c742a/aih-tih-sc-3270ab-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-3270ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled