Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/531ce8eeed88d6bca2bd96f40e7f0c/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f789d11d3dfd58975ba1c1dd754edc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/bb9193337bb6a2d42124dff24c3439/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/64bb71db35614ee027015bc4586297/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/bb9193337bb6a2d42124dff24c3439/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000