Ubooquity ran out of memory when scanning one of your PDF files.
On which kind of hardware are you running Ubooquity ? The info that I need is printed to the log file just after startup (Max heap size available, Java version, OS Name etc.)
If you want you can send me the full log file, I'll take a look. (PM)
In the meantime, you can also try to increase the quantity of memory Ubooquity is allowed to use.
See this FAQ entry.