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/9e/545a53dd7bc6696a4620748fc71381/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/545a53dd7bc6696a4620748fc71381/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/65f06cd3e9e66d1e34a7491dc5105b/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e106d13faaf71d982b3721a6e6dcf1/BreastNB_FFPE_L02_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: BreastNB_FFPE_L02_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