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Core dump when using GATK 3.7 haplotyper

I'm using gatk 3.7, java 1.8, human genome. For specific regions I'm using ploidy more than 2 due to specific aim of the question.

/usr/bin/java -Xmx10G -jar /mnt/mfs/hgrcgrid/shared/softwares/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller -R CR1_region1.ploidy_6.fa -I washei36472_ploidy6CR1region1.bam -L CR1_region1.expanded.bed --sample_ploidy 6 --genotyping_mode DISCOVERY --emitRefConfidence GVCF --dontUseSoftClippedBases -o washei36472.3CR1region1.g.vcf

Sorry, I can't quote/highlight text for code and error using github text guidelines. GATK forum didn't allow me to post link, maybe because my account is new.

I tried with 6G, 3G, 10G, 8G. The input bam and bed files are less than 1MB individually, I don't know what's the problem and how to fix it. If I use -nct flag either the error persists. I'm working on cluster node with 15G of memory, so I can easliy provide below 10G when running GATK.

Error log on screen:

Using AVX accelerated implementation of PairHMM
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00002b17edc60ce9, pid=30033, tid=0x00002b178ef5c700
# JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151-8u151-b12-1~deb9u1-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [] LoadTimeInitializer::LoadTimeInitializer()+0x1669
# Core dump written. Default location: /mnt/mfs/hgrcgrid/shared/GT_ADMIX/INDEL_comparisons/sequencing_projects/darkgenome/internal_pipeline/align_CR1exons/core or core.30033
# An error report file with more information is saved as:
# /mnt/mfs/hgrcgrid/shared/GT_ADMIX/INDEL_comparisons/sequencing_projects/darkgenome/internal_pipeline/align_CR1exons/hs_err_pid30033.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.

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