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/79/d34118de0ace6274835e3c5fd0fc44/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/0e875cb50de5e926b2780a973f1280/786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/d34118de0ace6274835e3c5fd0fc44/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/0a564da64801430f766c7668398f5b/786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled