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IndelRealigner Crashing, Java Fatal Error

Hello GATK,

I am receiving the following error when running this script:

java -Xmx32G -Djava.io.tmpdir=/data1/home/nipm/arvin/tmp \
-jar /data1/APPS/gatk_nightly/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R /data1/DATA/REFERENCE/human_g1k_v37_decoy.fasta \
-targetIntervals S14_03B_CHG000251_realignment_targets.list \
-known /data1/DATA/REFERENCE/1000G_phase1.indels.b37.vcf \
-I S14_03B_CHG000251_combined_dedup.bam \
-o S14_03B_CHG000251_indelrealigner.bam

INFO 18:21:42,635 ProgressMeter - 1:184280371 4.010121E7 33.9 m 50.0 s 5.9% 9.6 h 9.0 h
INFO 18:22:12,636 ProgressMeter - 1:187049819 4.0801219E7 34.4 m 50.0 s 6.0% 9.6 h 9.0 h
INFO 18:22:43,558 ProgressMeter - 1:190054021 4.1601238E7 34.9 m 50.0 s 6.1% 9.6 h 9.0 h
INFO 18:23:13,561 ProgressMeter - 1:192972143 4.2301251E7 35.4 m 50.0 s 6.2% 9.6 h 9.0 h
INFO 18:23:20,807 IndelRealigner - Not attempting realignment in interval 1:193831502-193831691 because there are too many reads.
INFO 18:23:43,562 ProgressMeter - 1:195808771 4.3001259E7 35.9 m 50.0 s 6.2% 9.6 h 9.0 h
#

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

#

SIGSEGV (0xb) at pc=0x00007fec98d8689b, pid=11969, tid=0x00007fec94265700

#

JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)

Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 )

Problematic frame:

V [libjvm.so+0x62e89b]

#

Core dump written. Default location: /data2/travis/WGS-86/CHG000251/core or core.11969

#

An error report file with more information is saved as:

/data2/travis/WGS-86/CHG000251/hs_err_pid11969.log

#

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

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

I am running GATK 3.8, nightly build from 09/18/2017

As for java:
openjdk version "1.8.0_144"
OpenJDK Runtime Environment (build 1.8.0_144-b01)
OpenJDK 64-Bit Server VM (build 25.144-b01, mixed mode)

I am trying to use 3.8 because 3.7 keeps crashing at HaplotypeCaller. I am now trying 3.7 using the flag --pair_hmm_implementation LOGLESS_CACHING, as this was a suggestion from my server administrator. She was also running into problems with HaplotypeCaller and this fixed her issue.

Answers

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