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

Core dump with HaplotypeCaller using GATK 3.7

I'm trying to run HaplotypeCaller on a single RNAseq BAM file, but I keep getting a core dump. I've tried allocating more memory (up to 150 GB RAM) and reverting to single-thread mode, but HaplotypeCaller continues to fail. I've other tools in GATK on this sample on this machine, and haven't had this issue.

% java -jar GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T HaplotypeCaller -R GRCh38_full_analysis_set_plus_decoy_hla.fa -I EC11.GRCh38_filtered_split_recal.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o EC11.GRCh38_filtered_split_recal.vcf -nct 16
Picked up _JAVA_OPTIONS: -Xmx64g
INFO  15:33:39,894 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:33:39,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
INFO  15:33:39,896 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  15:33:39,896 HelpFormatter - For support and documentation go to 
INFO  15:33:39,897 HelpFormatter - [Fri Jan 26 15:33:39 EST 2018] Executing on Linux 3.10.0-693.2.2.el7.x86_64 amd64 
INFO  15:33:39,897 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 
INFO  15:33:39,900 HelpFormatter - Program Args: -T HaplotypeCaller -R /gpfs/commons/home/hoffmanp-420/ALS/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /gpfs/commons/home/hoffmanp-420/ALS/Recalibrated/EC11.GRCh38_filtered_split_recal.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -o /gpfs/commons/home/hoffmanp-420/ALS/RawVCF/EC11.GRCh38_filtered_split_recal.vcf -nct 16 
INFO  15:33:39,904 HelpFormatter - Executing as on Linux 3.10.0-693.2.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14. 
INFO  15:33:39,904 HelpFormatter - Date/Time: 2018/01/26 15:33:39 
INFO  15:33:39,904 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:33:39,905 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:33:39,922 GenomeAnalysisEngine - Strictness is SILENT 
INFO  15:33:52,760 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500 
INFO  15:33:52,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  15:33:52,937 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17 
INFO  15:33:53,231 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 
INFO  15:33:53,263 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 16 CPU thread(s) for each of 1 data thread(s), of 40 processors available on this machine 
INFO  15:33:54,300 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  15:33:55,538 GenomeAnalysisEngine - Done preparing for traversal 
INFO  15:33:55,538 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining 
INFO  15:33:55,539 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime 
INFO  15:33:55,539 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output 
INFO  15:33:55,583 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
WARN  15:33:55,584 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples. 
INFO  15:33:55,584 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
INFO  15:33:55,781 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units 
INFO  15:33:55,782 PairHMM - Performance profiling for PairHMM is disabled because the program is being run with multiple threads (-nct>1) option
Profiling is enabled only when running in single thread mode

Using AVX accelerated implementation of PairHMM
# A fatal error has been detected by the Java Runtime Environment:
#  SIGSEGV (0xb) at pc=0x00007faa12753ce9, pid=31376, tid=140368447252224
# JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 )
# Problematic frame:
# C  []  LoadTimeInitializer::LoadTimeInitializer()+0x1669
# 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:
# /gpfs/commons/home/hoffmanp-420/ALS/hs_err_pid31376.log
# If you would like to submit a bug report, please visit:
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

I'm using Java 1.8.0_45 on CentOS 7.4.1708. My machine has 40 cores and 256 GB RAM.

Best Answer


Sign In or Register to comment.