processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 659_cX2_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam.bai
processing 659_cX2_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam ... Finished