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A fatal error has been detected by the Java Runtime Environment

dbeckerdbecker MunichMember ✭✭✭
edited October 2017 in Ask the GATK team

Hi,

Since a few days GATK crashes at PrintReads with a fatal java error.
We tried GATK 3.7 and 3.8; OpenJDK 1.8.0_144, Oracle JDK 1.8.0_102, OracleJRE 1.8.0_144 and 1.8.0_102 and we always get the same result.
We also did a memtest86+ without any result.

The log I attached shows an index out of bounds exception:

Event: 1,958 Thread 0x00007f91b000a000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 18> (0x00007f8c53d9d708) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u102/7268/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 1,958 Thread 0x00007f91b000a000 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 67> (0x00007f8c53d9ea20) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u102/7268/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]

Stdout:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f91b7b4b02b, pid=11948, tid=0x00007f819309e700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_102-b14) (build 1.8.0_102-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.102-b14 mixed mode linux-amd64 )
# Problematic frame:
# V  [libjvm.so+0x64802b]  InstanceKlass::oop_follow_contents(ParCompactionManager*, oopDesc*)+0x16b
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /srv/samba/ngsdata/toolbox/gatk/cromwell-executions/run_wdl_gatk/0b23a7d0-17eb-45e2-b81b-c61eaa37e6fb/call-baseRecalibrationPrint/shard-2/execution/hs_err_pid11948.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

Stderr:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/srv/samba/ngsdata/toolbox/gatk/cromwell-executions/run_wdl_gatk/0b23a7d0-17eb-45e2-b81b-c61eaa37e6fb/call-baseRecalibrationPrint/shard-2/execution/tmp.RsnOwJ
INFO  22:34:36,197 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  22:34:36,199 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 
INFO  22:34:36,199 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  22:34:36,199 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  22:34:36,199 HelpFormatter - [Sat Sep 30 22:34:36 CEST 2017] Executing on Linux 3.10.0-693.2.2.el7.x86_64 amd64 
INFO  22:34:36,199 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14 
INFO  22:34:36,203 HelpFormatter - Program Args: -T PrintReads -R /srv/samba/ngsdata/genome_builds/GRCh38_final.fa -I /srv/samba/ngsdata/GATK/170731_NS500396_0228_AHKL5MBGX2/_gatk/1724-0620-WholeExome-170731_NS500396_0228_AHKL5MBGX2_sorted.bam -BQSR /srv/samba/ngsdata/GATK/170731_NS500396_0228_AHKL5MBGX2/_gatk/1724-0620-WholeExome-170731_NS500396_0228_AHKL5MBGX2_recal_data.table -o /srv/samba/ngsdata/GATK/170731_NS500396_0228_AHKL5MBGX2/_gatk/1724-0620-WholeExome-170731_NS500396_0228_AHKL5MBGX2_recal_reads.bam 
INFO  22:34:36,209 HelpFormatter - Executing as [email protected] on Linux 3.10.0-693.2.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14. 
INFO  22:34:36,209 HelpFormatter - Date/Time: 2017/09/30 22:34:36 
INFO  22:34:36,209 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  22:34:36,209 HelpFormatter - ---------------------------------------------------------------------------------- 
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/opt/gatk/3.8-0-ge9d806836/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO  22:34:36,356 GenomeAnalysisEngine - Deflater: IntelDeflater 
INFO  22:34:36,356 GenomeAnalysisEngine - Inflater: IntelInflater 
INFO  22:34:36,358 GenomeAnalysisEngine - Strictness is SILENT 
INFO  22:34:36,720 ContextCovariate -       Context sizes: base substitution model 2, indel substitution model 3 
INFO  22:34:36,764 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  22:34:36,773 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:34:38,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.94 
INFO  22:34:38,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  22:34:38,807 GenomeAnalysisEngine - Done preparing for traversal 
INFO  22:34:38,807 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  22:34:38,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  22:34:38,808 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime 
INFO  22:34:38,815 ReadShardBalancer$1 - Loading BAM index data 
INFO  22:34:38,815 ReadShardBalancer$1 - Done loading BAM index data 
INFO  22:35:08,815 ProgressMeter -    chr1:1309615    100008.0    30.0 s       5.0 m        0.0%    19.7 h      19.6 h 
/usr/bin/gatk: Zeile 5: 11948 Abgebrochen             java $JAVAOPTS -jar /opt/gatk/3.8-0-ge9d806836/GenomeAnalysisTK.jar [email protected]

Thanks & best regards,
Daniel

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