Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/8fd7106cf7e20f5814371d1d6cdcd1/659_bIB-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/02/ec391bde20472e53a007914be63077/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/ec391bde20472e53a007914be63077/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/42fc06852d2ba0b299a3767fdc66df/659_bIB-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_bIB-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