processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s48.Aligned.sortedByCoord.out.bam.bai
processing GM24385_0001_RNA_0001_23H5VFLT4_s48.Aligned.sortedByCoord.out.bam ... Finished