at java.base/java.util.concurrent.FutureTask.report(Unknown Source) at java.base/java.util.concurrent.FutureTask.get(Unknown Source) at edu.umich.andykong.msfragger ...

I'd say the problem is that you're even dealing with a 2Gb XML file to begin with. XML is designed mostly as a method to exchange data between programs. What it looks like you're doing here is using ...