Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/afd9e5adf4029fe6dd9c25524bee53/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  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/d7/9665435f2c17da37c8d0c5eac39db5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/3a851a4d8450274f6ecb0fca9f923e/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9665435f2c17da37c8d0c5eac39db5/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled