processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_40C_2.Aligned.sortedByCoord.out.bam.bai
processing RGB_RLP_lowDV_1ststrand_40C_2.Aligned.sortedByCoord.out.bam ... Finished