processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
processing 786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam ... Finished