Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/e88fd7fc7045f143707b3a331bf8bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/14b57d5368a1a899a74376621da109/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/0db812b4930a2ff0552f60936bec40/tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/14b57d5368a1a899a74376621da109/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/3eea96f2119946dc75e6181a511bc1/tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000