How big of a FASTA file are you using?

That error seems to be a Java out of memory error happening while EncylopeDIA is figuring out which peptides are in the FASTA file.

I can see from the log file that the "ConvertBLIBToLibrary" task has been told to use about 6GB ("-Xmx6098M").
The amount of memory that Skyline tells EncyclopeDIA to use is the smaller of either 12GB or half of the memory in your computer.
This might succeed if you tried it on a computer that had at least 24GB of RAM.
-- Nick