processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
processing BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam ... Finished