Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/d49d68ff3e71b0706047dace7d2f15/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ead7548c923424c68495c616845975/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/32473d0374abcf43973e4cfabf5269/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/d49d68ff3e71b0706047dace7d2f15/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/dddecfed4a6c1f41ac206034711c4b/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000