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/bf/315affd1e0523d56743fb847409c09/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/315affd1e0523d56743fb847409c09/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/63df0e76099b03c47ce9f2cdcaf083/aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/a0688930551e426909ca1d9d6d7364/aih-tih-sc-01c779-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-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