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 -Djava.io.tmpdir=/gpfs/commons/home/hoffmanp-420/ALS/tmp.DpVNrl7ouV
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 https://software.broadinstitute.org/gatk 
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 [email protected] 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 - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
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  [libVectorLoglessPairHMM4517799834894878366.so+0x1bce9]  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:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted

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

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