Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/95ec88a9ce11301a20d4ffcb5030a5/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/d23339b8a327057c4d8e619ae64e63/659_ciZ-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/67/77c4f61ad001898470d46554176530/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/77c4f61ad001898470d46554176530/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_ciZ-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