processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
processing BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam ... Finished