Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/51a801f44b82a09301106ce3f6c001/BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.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/8e/672306414d777cb5a5f28979717e38/BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/dd9e62cad74cc62dc8b8538508c415/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/dd9e62cad74cc62dc8b8538508c415/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled