Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/e43f0a9041cb491576a1982bedd2fe/tih_rna_sample_00096_23H5VFLT4_s11.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/3d/ed192c66feac41815b478ce5a12b20/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/bb2c44ace0ead90c965921f3266c26/tih_rna_sample_00096_23H5VFLT4_s11.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/ed192c66feac41815b478ce5a12b20/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00096_23H5VFLT4_s11.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled