Hi @Martyn
What happens if your run a tool like Fasta Statistics on the data? Can that tool understand the data in your collections or does it report a problem? If it runs, does anything else look unexpected in the summary?
I am also curious about what happens if you try to run on just one genome file?
You are welcome to share the EU history back. Please leave the subset and statistics job in there too please. Maybe we can help to recognize what the problem is.
How to share is in the banner of this forum, also here → How to get faster help with your question
Thanks! 