[galaxy-user] Cuffmerge not working with reference genome

Dear All when I run Cuffmerge using the latest GenCode v19 GTF as a reference genome….this fails to run…tried this using multiple approaches and datasets. Of note…...Cuffmerge works fine when the Gencode GTF is omitted as a reference genome. CuffCompare also works fine when the same Gencode GTF is used as a reference genome. Presumably there is something wrong with the Cuffmerge set-up relating to the reference genome? Or am I doing something wrong. Best wishes Mark