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/e1/3cc24fdfe033e0e4e645e88d98501a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/3cc24fdfe033e0e4e645e88d98501a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/708828745aa92ea96e9a7231bb51c7/tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/f63ee4c7bdb5db7845b878969ce73b/tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000