Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/ff83ea30d2a8cc1a235dc7c8126eb3/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  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/ac/371cd13951048623f0b55018376041/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/371cd13951048623f0b55018376041/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/b8f8c87dd09599a9c5c0311e2153b1/659_b7Z-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_b7Z-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