Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/a0f89b39dab3e31a4376f94755f168/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/ba9b920cffe23f04e8893f19642591/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/5456459721e32009e1450f612c5ab7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/5456459721e32009e1450f612c5ab7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3c15023005fc6ecaab130723455b3f/rna_s1221_S42.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
processing rna_s1221_S42.Aligned.sortedByCoord.out.bam ... Finished