Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/e85caf98ee23a09a0c80d541fe28ad/659_cTi-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/32/8be43d391cfd57d5860f5b8f845a97/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/8be43d391cfd57d5860f5b8f845a97/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/446451d3d89ff3671a2d60ed9f0977/659_cTi-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000