processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
processing aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam ... Finished