Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/7e00883c5855145cdfdb184e7505f2/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/1e2fcf1754af77a22a09e2e77c303e/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/9e2a233ad9f3ec7826780d518e351d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/9e2a233ad9f3ec7826780d518e351d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/6ed28fc3a27c2ed6889fd01426200d/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