Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/42714a2da9de9f68f196a07b83a733/tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/9055d4b0da3d2fb2a1c6cf662c7616/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/a9c68c0d7d82fde47737457b37b96f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/a9c68c0d7d82fde47737457b37b96f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/470633ec6875aa44e851b44cd7b6c7/tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000