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

[Programjackanapes]

Bug Report

Affected tool(s)

Tool Name : SortSam MergeBamAlignment
Special Parameters : VALIDATION_STRINGENCY=LENIENT USE_JDK_DEFLATER=true USE_JDK_INFLATER=true
I tried USE_JDK_DEFLATER=true USE_JDK_INFLATER=true and VALIDATION_STRINGENCY=LENIENT but they didn't work.

Affected version

Picard 2.27.1, 2.18.0,1.141
I tried Java 1.7, 1.8 ,Java 11 and Java 18, they didn't work.

Description

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

SIGSEGV (0xb) at pc=0x00002afb85608023, pid=15243, tid=0x00002afb83dbc180

JRE version: Java(TM) SE Runtime Environment (8.0_331-b09) (build 1.8.0_331-b09)

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.331-b09 mixed mode linux-amd64 compressed oops)

Problematic frame:

V [libjvm.so+0x915023] SR_handler(int, siginfo*, ucontext*)+0x33

Core dump written. Default location: /home/scjidet/A_Test_For_Pipline/11909_MSS/normal/align/bam/02_PicardStep_SortSam/core or core.15243

If you would like to submit a bug report, please visit:

http://bugreport.java.com/bugreport/crash.jsp

Steps to reproduce

java -jar /Software/picard.jar SortSam INPUT=../11909_MSS_normal.aligned.bam OUTPUT=11909_MSS_normal.aligned.sorted.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT USE_JDK_DEFLATER=true USE_JDK_INFLATER=true

[Programjackanapes]

It's very strange that when I run on my computer, there is no problem at all, but an error occurs when I submit to the computing node.

[Programjackanapes]

hs_err_pid3059.log

[solivehong]

I'm having the same issue on a compute node, a standalone compute server works fine, using udocker with gatk 4 2.6.1