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/08/3918923025148acc244d229e0ac24d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/3918923025148acc244d229e0ac24d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/5ef34901cf4eadded45cac52de7e0c/659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/6a433b48423cb1b81bcb42ff22b6ec/659_bKP-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_bKP-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