Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/f73a0e22861201cc7c5cccf07ed1b4/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/cda4df935f0982ceff90a973cc9044/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/cda4df935f0982ceff90a973cc9044/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/4c58821c404301a6ebc40f9006e4c7/659_bTo-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/d59008557cbe3bc28efb8f92e23833/659_bTo-T1-TRNA-1_A23MVY2LT4_2.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_bTo-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
processing 659_bTo-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam ... Finished