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Unexpected java error with GATK DepthOfCoverage

I am calculating DepthOfCoverage from a bam file generated on a SOLID 5500. I have used this tool before with this file and had no problems. I find now that java errors out after reading traversing the file. The warning I receive is as follows:

"An unexpected error has been detected by Java Runtime Environment:

Internal Error (exceptions.cpp:367), pid=1612, tid=1081166144
Error: ExceptionMark destructor expects no pending exceptions"

I reported the crash to java. Any insights on what is causing this error and how it can be resolved?



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