Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/b02a7396bf6caf366aae276126d7b9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/893c48087adf1965d06d3afa2da649/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/893c48087adf1965d06d3afa2da649/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/75c67cbabe686568cf36118f80926b/659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/efa3af46df2de4cdb0bc3e1db16b14/659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
processing 659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam ... Finished