processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
processing 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam ... Finished