Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/6b8ed2af8db4aec0135c02d1be12b3/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/09587d62b8784d7409f150baef3d2b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/09587d62b8784d7409f150baef3d2b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/3e8a82e76bbc12a902ec65f52defc1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled