processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
processing 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam ... Finished