I’m using galaxy for my Genomics course. We are currently working on our annotation unit. Every time I try to run gffread the job looks like it will start, but then never actually updates in my history. I do not get an error message at all. I’ve been able to run other tools without any issues.
You need to select one of the options that produces an output, e.g. the options under Feature File Output, or the options available if you specify a reference genome.