Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/50ce38a6df36119b17bb2e96d5f5af/659_bGW-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/374e727a4ddaf2a18e012312de3780/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/f73a0e22861201cc7c5cccf07ed1b4/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/374e727a4ddaf2a18e012312de3780/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/e822b73d09ba71829a7ea4ecc56fb6/659_bGW-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled