processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
processing BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam ... Finished