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HaplotypeCaller error: A fatal error has been detected by the Java Runtime Environment

ktrp90ktrp90 kongkongMember ✭
in Ask the GATK team

Hi,

When I am using HaplotypeCaller on a recently updated system, I always got an error message like this:

#

A fatal error has been detected by the Java Runtime Environment:

#

SIGSEGV (0xb) at pc=0x00007ff0d6126ce9, pid=30388, tid=0x00007ff10e748700

#

JRE version: Java(TM) SE Runtime Environment (8.0_131-b11) (build 1.8.0_131-b11)

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.131-b11 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [libVectorLoglessPairHMM442890693276836996.so+0x1bce9] LoadTimeInitializer::LoadTimeInitializer()+0x1669

Does anybody know what is the cause of the problem? Are there any fix to it?

Thanks,

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