The RNASTAR jobs started less than 14 hours ago are still queued and the other mapping jobs started a few hours ago (Bowtie2/BWA-MEM) are currently executing. These likely were sent to different clusters. There are no known issues right now, but we are double checking and will post an update if a problem is discovered.
I did notice that the custom reference genome is not in fasta format. It is instead a count of the lines of the original fasta dataset. This means that all jobs will end up failing, both those that are queued and those that are executing. All will need to be permanently deleted and rerun using a valid fasta formatted custom reference genome.
Thanks! Jen, Galaxy team