Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/9c3b58ad3ad1c96a56aaf93e7daab6/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/0a96b55d84d45d8460e84d472820bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e15b5088747d7eff8f534cc098be81/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e15b5088747d7eff8f534cc098be81/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/ee962920b4c920a2ad9202321cdc6d/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled