Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/7b351d8ea47e284bb7ddbc8e502642/659_bTq-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/a7/ff75f526ec98e61d151054b645a436/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/ff75f526ec98e61d151054b645a436/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/9db99f4569182b6013f8a3241901a4/659_bTq-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_bTq-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