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Loading Native Libraries causes segfault #4158
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@gspowley Could you and your team please have a look a this one? |
The segfault happens in
Here's similar issue, which also used Alpine Linux: bytedeco/javacv#716. The resolution was to move to a different Linux distro. @apeltzer, assuming you want to use Alpine, please try running without |
I'll test and let you know asap. Thanks for the hint! |
Unfortunately, that doesn't resolve the issue. I'll see whether I can put some logs together to get you a better overview. |
Hi!
I've created a container using Singularity and Alpine Linux 3.7, including all the mentioned dependencies for GATK 4.0.0.0 (JDK8, GCC, R, R-Dev, Python, libgomp) and tried running HaplotypeCaller on a sample of mine to test everything.
Unfortunately, it always breaks when running the steps with the JNI libraries. If I start running things on native Java (without the C++ libraries), things work well.
I copied my log file and the command + hs_err file in here.
Anything I missed here?
Here's the
hs_err
file:The text was updated successfully, but these errors were encountered: