Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/efedf9c256727b30ecd682c62a130f/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/ac94aee4eb82a2358c130d4f3c8838/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/73/abbe94d9d871b1b6fe27b7fa2f614d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/abbe94d9d871b1b6fe27b7fa2f614d/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-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