Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/d33bc63f9d672642cc5d74171216f1/659_8h-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  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/fe/f017d44553493afa03c7dd859266e5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/f017d44553493afa03c7dd859266e5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/c8d6e2baece2b1cdc4db5c596e034e/659_8h-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

Get exon regions from ref_annot.bed ...
Load BAM file ...  Done
Total read pairs  used 4144