processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam.bai
processing HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam ... Finished