Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/e7f0deb18cfa7ccd673016df7bee22/659_zC_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/004a12a7af3e1ecdb989b931a6b2a9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/dde390b8ccabf25ecbe259fe177999/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/ce9740df0ced31e3349989be343e21/659_zC_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/dde390b8ccabf25ecbe259fe177999/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_zC_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000