Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/b32f1613cc5cc643875b9ddf6bf94e/659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/03cafb423c59e14fcbd4a149a5cb07/659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/0243baf59143a09530ee8911e13e43/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c6761b06acd756d6a5301e0bf89814/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c6761b06acd756d6a5301e0bf89814/.command.run
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
processing 659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam ... Finished