Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/3243ec3aa229936f9d97ea86dae11b/659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/0243baf59143a09530ee8911e13e43/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/18419ca9be78ff7e9dc23cf7aa6e30/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/18419ca9be78ff7e9dc23cf7aa6e30/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/e4b6bb64305bfbe210bc6de3e33c24/659_bCu-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_bCu-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