Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/80660f98e0eb402bd0bfaf242a5a73/659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  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/78/79803e0f37d82d9c2835eb1c449a02/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/79803e0f37d82d9c2835eb1c449a02/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/197b5f057a677ec6dbf9ec3464f10d/659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

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