Hello,
Could you please help me to figure out this fatal error in running PrintReads?
After I updated GATK to version 3.8-0. I kept getting this fatal error in running PrintReads. I can skip this step and run HaplotypeCaller with -BQSR option.
parsing sample: SRR098333
INFO 17:12:12,287 HelpFormatter - ----------------------------------------------------------------------------------
INFO 17:12:12,289 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 17:12:12,289 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 17:12:12,289 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 17:12:12,289 HelpFormatter - [Sat Sep 09 17:12:12 EDT 2017] Executing on Linux 2.6.32-358.23.2.el6.x86_64 amd64
INFO 17:12:12,289 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17
INFO 17:12:12,293 HelpFormatter - Program Args: -T PrintReads -nct 8 -R ./refs/GATK_Resource_Bundle/b37/human_g1k_v37.fasta -BQSR SRR098333.recal_data.table -I SRR098333.bwa_mem.sorted_dups_removed_indelrealigner.bam -o SRR098333.bwa_mem.sorted_dups_removed_indelrealigner_BQSR.bam
...
INFO 17:43:53,363 ProgressMeter - 3:83180289 4.6776207E7 31.7 m 40.0 s 18.6% 2.8 h 2.3 h
#
A fatal error has been detected by the Java Runtime Environment:
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SIGSEGV (0xb) at pc=0x00007fe6c2da3f8b, pid=1932, tid=140629048932096
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JRE version: Java(TM) SE Runtime Environment (8.0_65-b17) (build 1.8.0_65-b17)
Java VM: Java HotSpot(TM) 64-Bit Server VM (25.65-b01 mixed mode linux-amd64 )
Problematic frame:
V [libjvm.so+0x64bf8b] InstanceKlass::oop_follow_contents(ParCompactionManager*, oopDesc*)+0x16b
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Core dump written. Default location: core or core.1932
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An error report file with more information is saved as:
hs_err_pid1932.log
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If you would like to submit a bug report, please visit:
http://bugreport.java.com/bugreport/crash.jsp
#
/var/spool/slurmd/job465052/slurm_script: line 18: 1932 Aborted (core dumped) java -Xms16g -Xmx200g -jar /home/apps/GATK/GenomeAnalysisTK-3.8.0/GenomeAnalysisTK.jar -T PrintReads -nct 8 -R ./refs/GATK_Resource_Bundle/b37/human_g1k_v37.fasta -BQSR SRR09833$SLURM_ARRAY_TASK_ID.recal_data.table -I SRR09833$SLURM_ARRAY_TASK_ID.bwa_mem.sorted_dups_removed_indelrealigner.bam -o SRR09833$SLURM_ARRAY_TASK_ID.bwa_mem.sorted_dups_removed_indelrealigner_BQSR.bam