processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2905df-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
processing aih-tih-sc-2905df-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam ... Finished