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/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/17/0a96b55d84d45d8460e84d472820bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/a4e1dd8e0e44273447b1c0b54b0754/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/a4e1dd8e0e44273447b1c0b54b0754/.command.run
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[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
processing BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam ... Finished