To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Segfault when running GATK 3.6 in a container

I'm using GATK on the DNAnexus platform, which can convert Docker images to the ACI format in order to run them. I have a Docker image that uses GATK 3.6 to call variants, which runs fine under ordinary Docker, but which segfaults when run on DNAnexus using this converted container format.

The log for this error is attached. The key information is this:

#  SIGSEGV (0xb) at pc=0x00007f3980e9dce9, pid=17744, tid=0x00007f39a146a700
# JRE version: OpenJDK Runtime Environment (8.0_141-b15) (build 1.8.0_141-8u141-b15-1~deb9u1-b15)
# Java VM: OpenJDK 64-Bit Server VM (25.141-b15 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  []  LoadTimeInitializer::LoadTimeInitializer()+0x1669

So, it seems that somehow the compiled C code in GATK is having troubles under this specific environment. How should I attempt to resolve this? Should I upgrade or downgrade Java? GATK? Ubuntu? System libraries? Unfortunately upgrading GATK would be a bit difficult, because our workflow is accredited using GATK 3.6, but this might be possible if this is the only solution.


Sign In or Register to comment.