Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/c7b2e2a855df39ae1448bba993a256/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/2685a0cad37f71d2dcd023e3833915/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/e30a2c322beae0fe39937d1e7e3013/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/e30a2c322beae0fe39937d1e7e3013/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/7a0d41f32cf8151d25c77b4b0ffdd7/rna_s1221_S42.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000