Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/e18e7faa417fcf27aed7f62fac831b/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/ea7e1bfd07612c80b138d796182949/aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  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/43/1007dd5f727139200c35b0ad98fb5c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/1007dd5f727139200c35b0ad98fb5c/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01eb49-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