processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam.bai
processing tih_rna_sample_00111_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam ... Finished