HaplotyopeCaller SIGSEGV error in small region across multiple samples
Hello! I'm trying to run GATK HaplotypeCaller on PacBio HiFi data aligned to T2TCHM13v2.0, something I've done many times before. I'm currently working on a family with about 20 samples, but for 5 samples, I'm getting an error I've never seen before. I've narrowed the problem down to a 100kb region - chr7:135400000-135500000 - with the exact last coordinate output in the resulting gvcf varying a little between attempts. In all 5 samples, HaplotypeCaller fails in this region, and Java spits out a SIGSEGV error. It works just fine on chr7 before and after this region, but I always get the same error here. I've checked the input BAM file and I've looked at the region in IGV to make sure it looks normal, so I don't think the problem should be coming from the input.
REQUIRED for all errors and issues:
a) GATK version used:
v4.4.0.0 and v4.3.0.0
b) Exact command used:
gatk --java-options "-Xmx800G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" HaplotypeCaller --native-pair-hmm-threads 1 --reference /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/platinum_genomes/chm13v2.0_maskedY_rCRS.fa.gz --input /net/eichler/vol28/projects/platinum_genomes/nobackups/denovo/alignment/hifi/CHM13_v2.0/K1463_2281_ccs_to_chm13.bam --output K1463.2281.chr7_part_2c.g.vcf.gz --pcr-indel-model AGGRESSIVE --intervals chr7_part_2c.bed --minimum-mapping-quality 60 --read-filter MappingQualityReadFilter --read-filter NotSecondaryAlignmentReadFilter --read-filter NotSupplementaryAlignmentReadFilter -ERC GVCF
c) Entire program log:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007e376e5f70fb, pid=141529, tid=141589
#
# JRE version: OpenJDK Runtime Environment 21.9 (18.0.1+10) (build 18.0.1+10)
# Java VM: OpenJDK 64-Bit Server VM 21.9 (18.0.1+10, mixed mode, sharing, tiered, compressed class ptrs, g1 gc, linux-amd64)
# Problematic frame:
# C [libgkl_pairhmm_omp13802390137529139622.so+0x1c0fb] double compute_full_prob_avx512d<double>(testcase*)+0x37b
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/libexec/abrt-hook-ccpp %s %c %p %u %g %t e %P %I %h" (or dumping to /net/eichler/vol28/projects/platinum_genomes/nobackups/denovo/gatk/CHM13_v2.0/problems/core.141529)
#
# 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.
#
--------------- S U M M A R Y ------------
Command Line: -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx800G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true /net/eichler/vol26/7200/software/modules-sw/gatk/4.4.0.0/Linux/CentOS7/x86_64/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller --native-pair-hmm-threads 1 --reference /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/platinum_genomes/chm13v2.0_maskedY_rCRS.fa.gz --input /net/eichler/vol28/projects/platinum_genomes/nobackups/denovo/alignment/hifi/CHM13_v2.0/K1463_2281_ccs_to_chm13.bam --output K1463.2281.chr7_part_2c.g.vcf.gz --pcr-indel-model AGGRESSIVE --intervals chr7_part_2c.bed --minimum-mapping-quality 60 --read-filter MappingQualityReadFilter --read-filter NotSecondaryAlignmentReadFilter --read-filter NotSupplementaryAlignmentReadFilter -ERC GVCF
Host: Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz, 160 cores, 2015G, CentOS Linux release 7.9.2009 (Core)
Time: Wed Aug 23 14:09:33 2023 PDT elapsed time: 11.817000 seconds (0d 0h 0m 11s)
--------------- T H R E A D ---------------
Current thread (0x00007f084c014f20): JavaThread "main" [_thread_in_native, id=141589, stack(0x00007f0855d39000,0x00007f0855e3a000)]
Stack: [0x00007f0855d39000,0x00007f0855e3a000], sp=0x00007f0855d29850, free space=18014398509481922k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libgkl_pairhmm_omp13802390137529139622.so+0x1c0fb] double compute_full_prob_avx512d<double>(testcase*)+0x37b
C [libgkl_pairhmm_omp13802390137529139622.so+0x1500f] Java_com_intel_gkl_pairhmm_IntelPairHmm_computeLikelihoodsNative._omp_fn.0+0xcf
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j com.intel.gkl.pairhmm.IntelPairHmm.computeLikelihoodsNative([Ljava/lang/Object;[Ljava/lang/Object;[D)V+0
j com.intel.gkl.pairhmm.IntelPairHmm.computeLikelihoods([Lorg/broadinstitute/gatk/nativebindings/pairhmm/ReadDataHolder;[Lorg/broadinstitute/gatk/nativebindings/pairhmm/HaplotypeDataHolder;[D)V+26
j org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.computeLog10Likelihoods(Lorg/broadinstitute/hellbender/utils/genotyper/LikelihoodMatrix;Ljava/util/List;Lorg/broadinstitute/hellbender/utils/pairhmm/PairHMMInputScoreImputator;)V+231
j org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(Lorg/broadinstitute/hellbender/utils/genotyper/LikelihoodMatrix;)V+128
j org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(Ljava/util/List;Lhtsjdk/samtools/SAMFileHeader;Lorg/broadinstitute/hellbender/utils/genotyper/SampleList;Ljava/util/Map;Z)Lorg/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods;+78
j org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet;Lorg/broadinstitute/hellbender/utils/genotyper/SampleList;Ljava/util/Map;Z)Lorg/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods;+21
j org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(Lorg/broadinstitute/hellbender/engine/AssemblyRegion;Lorg/broadinstitute/hellbender/engine/FeatureContext;Lorg/broadinstitute/hellbender/engine/ReferenceContext;)Ljava/util/List;+1199
j org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(Lorg/broadinstitute/hellbender/engine/AssemblyRegion;Lorg/broadinstitute/hellbender/engine/ReferenceContext;Lorg/broadinstitute/hellbender/engine/FeatureContext;)V+7
j org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(Lorg/broadinstitute/hellbender/engine/MultiIntervalLocalReadShard;Lorg/broadinstitute/hellbender/engine/ReferenceDataSource;Lorg/broadinstitute/hellbender/engine/FeatureManager;)V+135
j org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse()V+83
j org.broadinstitute.hellbender.engine.GATKTool.doWork()Ljava/lang/Object;+19
j org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool()Ljava/lang/Object;+34
j org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs()Ljava/lang/Object;+225
j org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain([Ljava/lang/String;)Ljava/lang/Object;+14
j org.broadinstitute.hellbender.Main.runCommandLineProgram(Lorg/broadinstitute/hellbender/cmdline/CommandLineProgram;[Ljava/lang/String;)Ljava/lang/Object;+20
j org.broadinstitute.hellbender.Main.mainEntry([Ljava/lang/String;)V+22
j org.broadinstitute.hellbender.Main.main([Ljava/lang/String;)V+8
v ~StubRoutines::call_stub
siginfo: si_signo: 11 (SIGSEGV), si_code: 2 (SEGV_ACCERR), si_addr: 0x00007f0855d39000
Register to memory mapping:
RAX=0x0000000000000357 is an unknown value
RBX=0x00007f0855d2ba70 points into unknown readable memory: 0x7f2b4e81b4e81b4f | 4f 1b e8 b4 81 4e 2b 7f
RCX=0x00000000000006cb is an unknown value
RDX=0x00007f0855d39000 is pointing into the stack for thread: 0x00007f084c014f20
RSP=0x00007f0855d29850 points into unknown readable memory: 0x05000a011301813d | 3d 81 01 13 01 0a 00 05
RBP=0x00007f0855e37d70 is pointing into the stack for thread: 0x00007f084c014f20
RSI=0x000000000000365b is an unknown value
RDI=0x0000000000000002 is an unknown value
R8 =0x000000000000365c is an unknown value
R9 =0x0000000000000001 is an unknown value
R10=0x00007f0855d46d60 is pointing into the stack for thread: 0x00007f084c014f20
R11=0x00007f084d172820 points into unknown readable memory: 0x4154414754434754 | 54 47 43 54 47 41 54 41
R12=0x00007f0855d62050 is pointing into the stack for thread: 0x00007f084c014f20
R13=0x000000000001b2e8 is an unknown value
R14=0x000000000000365d is an unknown value
R15=0x00000fe10aba574e is an unknown value
Registers:
RAX=0x0000000000000357, RBX=0x00007f0855d2ba70, RCX=0x00000000000006cb, RDX=0x00007f0855d39000
RSP=0x00007f0855d29850, RBP=0x00007f0855e37d70, RSI=0x000000000000365b, RDI=0x0000000000000002
R8 =0x000000000000365c, R9 =0x0000000000000001, R10=0x00007f0855d46d60, R11=0x00007f084d172820
R12=0x00007f0855d62050, R13=0x000000000001b2e8, R14=0x000000000000365d, R15=0x00000fe10aba574e
RIP=0x00007e376e5f70fb, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000006
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00007f0855d29850)
0x00007f0855d29850: 05000a011301813d 2010000a60c00000
0x00007f0855d29860: 92afb49408364402 4840416084083ac0
0x00007f0855d29870: ffffffffffffffff 0002870555545006
0x00007f0855d29880: c15900008a280300 3ea400e000800850
Instructions: (pc=0x00007e376e5f70fb)
0x00007e376e5f6ffb: e8 90 84 ff ff 4c 8b 95 68 fe ff ff 4c 89 ea 31
0x00007e376e5f700b: f6 4c 89 d7 e8 7c 84 ff ff 49 89 c2 48 89 d8 44
0x00007e376e5f701b: 8b 85 50 fd ff ff 48 c1 e8 03 b9 09 00 00 00 48
0x00007e376e5f702b: f7 d8 83 e0 07 8d 50 07 c5 fb 10 85 10 fd ff ff
0x00007e376e5f703b: c5 fb 10 95 78 fe ff ff 83 fa 09 0f 42 d1 41 39
0x00007e376e5f704b: d0 0f 82 dc 18 00 00 85 c0 0f 84 ab 18 00 00 83
0x00007e376e5f705b: f8 01 c4 a1 7b 11 14 fd 00 00 00 00 0f 84 9f 18
0x00007e376e5f706b: 00 00 83 f8 02 c4 a1 7b 11 14 fd 08 00 00 00 0f
0x00007e376e5f707b: 84 b5 18 00 00 83 f8 03 c4 a1 7b 11 14 fd 10 00
0x00007e376e5f708b: 00 00 0f 84 28 18 00 00 83 f8 04 c4 a1 7b 11 14
0x00007e376e5f709b: fd 18 00 00 00 0f 84 bc 18 00 00 83 f8 05 c4 a1
0x00007e376e5f70ab: 7b 11 14 fd 20 00 00 00 0f 84 9f 18 00 00 83 f8
0x00007e376e5f70bb: 06 c4 a1 7b 11 14 fd 28 00 00 00 0f 84 a0 18 00
0x00007e376e5f70cb: 00 c4 a1 7b 11 14 fd 30 00 00 00 bf 07 00 00 00
0x00007e376e5f70db: 44 89 f6 62 f2 fd 48 19 ca 48 8d 14 c3 29 c6 31
0x00007e376e5f70eb: c0 89 f1 c1 e9 03 0f 1f 80 00 00 00 00 83 c0 01
0x00007e376e5f70fb: 62 f1 fd 48 29 0a 48 83 c2 40 39 c1 77 ef 89 f0
0x00007e376e5f710b: 83 e0 f8 01 c7 39 c6 0f 84 e0 00 00 00 48 63 c7
0x00007e376e5f711b: c5 fb 11 14 c3 8d 47 01 41 39 c6 0f 8e cc 00 00
0x00007e376e5f712b: 00 48 98 c5 fb 11 14 c3 8d 47 02 41 39 c6 0f 8e
0x00007e376e5f713b: b9 00 00 00 48 98 c5 fb 11 14 c3 8d 47 03 41 39
0x00007e376e5f714b: c6 0f 8e a6 00 00 00 48 98 c5 fb 11 14 c3 8d 47
0x00007e376e5f715b: 04 41 39 c6 0f 8e 93 00 00 00 48 98 c5 fb 11 14
0x00007e376e5f716b: c3 8d 47 05 41 39 c6 0f 8e 80 00 00 00 48 98 c5
0x00007e376e5f717b: fb 11 14 c3 8d 47 06 41 39 c6 7e 71 48 98 c5 fb
0x00007e376e5f718b: 11 14 c3 8d 47 07 41 39 c6 7e 62 48 98 c5 fb 11
0x00007e376e5f719b: 14 c3 8d 47 08 41 39 c6 7e 53 48 98 c5 fb 11 14
0x00007e376e5f71ab: c3 8d 47 09 41 39 c6 7e 44 48 98 c5 fb 11 14 c3
0x00007e376e5f71bb: 8d 47 0a 41 39 c6 7e 35 48 98 c5 fb 11 14 c3 8d
0x00007e376e5f71cb: 47 0b 41 39 c6 7e 26 48 98 c5 fb 11 14 c3 8d 47
0x00007e376e5f71db: 0c 41 39 c6 7e 17 83 c7 0d 48 98 41 39 fe c5 fb
0x00007e376e5f71eb: 11 14 c3 7e 08 48 63 ff c5 fb 11 14 fb 83 bd 10
Stack slot to memory mapping:
stack at sp + 0 slots: 0x05000a011301813d is an unknown value
stack at sp + 1 slots: 0x2010000a60c00000 is an unknown value
stack at sp + 2 slots: 0x92afb49408364402 is an unknown value
stack at sp + 3 slots: 0x4840416084083ac0 is an unknown value
stack at sp + 4 slots: 0xffffffffffffffff is an unknown value
stack at sp + 5 slots: 0x0002870555545006 is an unknown value
stack at sp + 6 slots: 0xc15900008a280300 is an unknown value
stack at sp + 7 slots: 0x3ea400e000800850 is an unknown value
--------------- P R O C E S S ---------------
Threads class SMR info:
_java_thread_list=0x00007e3718001a90, length=18, elements={
0x00007f084c014f20, 0x00007f084c2bafd0, 0x00007f084c2bc610, 0x00007f084c2c3ff0,
0x00007f084c2c5400, 0x00007f084c2c6900, 0x00007f084c2c84a0, 0x00007f084c2c9b20,
0x00007f084c2cb0a0, 0x00007e38780653b0, 0x00007f084c31e750, 0x00007f084c3219d0,
0x00007e38780d05a0, 0x00007e372c030010, 0x00007e3870027250, 0x00007e3878038ed0,
0x00007e3878039ed0, 0x00007e3860102c30
}
Java Threads: ( => current thread )
=>0x00007f084c014f20 JavaThread "main" [_thread_in_native, id=141589, stack(0x00007f0855d39000,0x00007f0855e3a000)]
0x00007f084c2bafd0 JavaThread "Reference Handler" daemon [_thread_blocked, id=141632, stack(0x00007e38a8c5e000,0x00007e38a8d5f000)]
0x00007f084c2bc610 JavaThread "Finalizer" daemon [_thread_blocked, id=141633, stack(0x00007e38a8b5d000,0x00007e38a8c5e000)]
0x00007f084c2c3ff0 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=141637, stack(0x00007e38a8a5c000,0x00007e38a8b5d000)]
0x00007f084c2c5400 JavaThread "Service Thread" daemon [_thread_blocked, id=141638, stack(0x00007e38a895b000,0x00007e38a8a5c000)]
0x00007f084c2c6900 JavaThread "Monitor Deflation Thread" daemon [_thread_blocked, id=141639, stack(0x00007e38a885a000,0x00007e38a895b000)]
0x00007f084c2c84a0 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=141640, stack(0x00007e38a8759000,0x00007e38a885a000)]
0x00007f084c2c9b20 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=141641, stack(0x00007e38a8658000,0x00007e38a8759000)]
0x00007f084c2cb0a0 JavaThread "Sweeper thread" daemon [_thread_blocked, id=141643, stack(0x00007e38a8557000,0x00007e38a8658000)]
0x00007e38780653b0 JavaThread "C1 CompilerThread1" daemon [_thread_blocked, id=141651, stack(0x00007e38a8456000,0x00007e38a8557000)]
0x00007f084c31e750 JavaThread "Notification Thread" daemon [_thread_blocked, id=141652, stack(0x00007e38a8355000,0x00007e38a8456000)]
0x00007f084c3219d0 JavaThread "Common-Cleaner" daemon [_thread_blocked, id=141654, stack(0x00007e38a8152000,0x00007e38a8253000)]
0x00007e38780d05a0 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=143358, stack(0x00007e3889181000,0x00007e3889282000)]
0x00007e372c030010 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=143590, stack(0x00007e38880c6000,0x00007e38881c7000)]
0x00007e3870027250 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=143829, stack(0x00007e38a8051000,0x00007e38a8152000)]
0x00007e3878038ed0 JavaThread "C1 CompilerThread4" daemon [_thread_blocked, id=143830, stack(0x00007e385bcf8000,0x00007e385bdf9000)]
0x00007e3878039ed0 JavaThread "C1 CompilerThread5" daemon [_thread_blocked, id=143831, stack(0x00007e376dbfe000,0x00007e376dcff000)]
0x00007e3860102c30 JavaThread "C1 CompilerThread6" daemon [_thread_blocked, id=143955, stack(0x00007e376d3f6000,0x00007e376d4f7000)]
Other Threads:
0x00007f084c2b77b0 VMThread "VM Thread" [stack: 0x00007e38a8d61000,0x00007e38a8e61000] [id=141631]
0x00007f084c320280 WatcherThread "VM Periodic Task Thread" [stack: 0x00007e38a8255000,0x00007e38a8355000] [id=141653]
0x00007f084c0a7180 WorkerThread "GC Thread#0" [stack: 0x00007f0830054000,0x00007f0830154000] [id=141617]
0x00007e389801d4e0 WorkerThread "GC Thread#1" [stack: 0x00007e385b9f5000,0x00007e385baf5000] [id=142608]
0x00007e389801dd70 WorkerThread "GC Thread#2" [stack: 0x00007e385b8f3000,0x00007e385b9f3000] [id=142609]
0x00007e389801e6f0 WorkerThread "GC Thread#3" [stack: 0x00007e385b7f1000,0x00007e385b8f1000] [id=142610]
0x00007e389801f230 WorkerThread "GC Thread#4" [stack: 0x00007e385b6ef000,0x00007e385b7ef000] [id=142611]
0x00007e389801fd70 WorkerThread "GC Thread#5" [stack: 0x00007e385b5ed000,0x00007e385b6ed000] [id=142612]
0x00007e38980208b0 WorkerThread "GC Thread#6" [stack: 0x00007e385b4eb000,0x00007e385b5eb000] [id=142613]
0x00007e38980213f0 WorkerThread "GC Thread#7" [stack: 0x00007e385b3e9000,0x00007e385b4e9000] [id=142614]
0x00007e3898021f50 WorkerThread "GC Thread#8" [stack: 0x00007e385b2e7000,0x00007e385b3e7000] [id=142615]
0x00007e3898022ad0 WorkerThread "GC Thread#9" [stack: 0x00007e385b1e5000,0x00007e385b2e5000] [id=142616]
0x00007e3898023650 WorkerThread "GC Thread#10" [stack: 0x00007e385b0e3000,0x00007e385b1e3000] [id=142617]
0x00007e38980241d0 WorkerThread "GC Thread#11" [stack: 0x00007e385afe1000,0x00007e385b0e1000] [id=142618]
0x00007e3898024d50 WorkerThread "GC Thread#12" [stack: 0x00007e385aedf000,0x00007e385afdf000] [id=142619]
0x00007e38980258d0 WorkerThread "GC Thread#13" [stack: 0x00007e385addd000,0x00007e385aedd000] [id=142620]
0x00007e3898026450 WorkerThread "GC Thread#14" [stack: 0x00007e385acdb000,0x00007e385addb000] [id=142621]
0x00007e38980273c0 WorkerThread "GC Thread#15" [stack: 0x00007e385abd9000,0x00007e385acd9000] [id=142622]
0x00007e3898028330 WorkerThread "GC Thread#16" [stack: 0x00007e385aad7000,0x00007e385abd7000] [id=142623]
0x00007e38980292a0 WorkerThread "GC Thread#17" [stack: 0x00007e385a9d5000,0x00007e385aad5000] [id=142624]
0x00007e389802a210 WorkerThread "GC Thread#18" [stack: 0x00007e385a8d3000,0x00007e385a9d3000] [id=142625]
0x00007e389802b180 WorkerThread "GC Thread#19" [stack: 0x00007e385a7d1000,0x00007e385a8d1000] [id=142626]
0x00007e389802c0f0 WorkerThread "GC Thread#20" [stack: 0x00007e385a6cf000,0x00007e385a7cf000] [id=142627]
0x00007e389802d060 WorkerThread "GC Thread#21" [stack: 0x00007e385a5cd000,0x00007e385a6cd000] [id=142628]
0x00007e389802dfd0 WorkerThread "GC Thread#22" [stack: 0x00007e385a4cb000,0x00007e385a5cb000] [id=142629]
0x00007e389802ef40 WorkerThread "GC Thread#23" [stack: 0x00007e385a3c9000,0x00007e385a4c9000] [id=142630]
0x00007e389802feb0 WorkerThread "GC Thread#24" [stack: 0x00007e385a2c7000,0x00007e385a3c7000] [id=142631]
0x00007e3898030e20 WorkerThread "GC Thread#25" [stack: 0x00007e385a1c5000,0x00007e385a2c5000] [id=142632]
0x00007e3898031d90 WorkerThread "GC Thread#26" [stack: 0x00007e385a0c3000,0x00007e385a1c3000] [id=142633]
0x00007e3898032d00 WorkerThread "GC Thread#27" [stack: 0x00007e3859fc1000,0x00007e385a0c1000] [id=142634]
0x00007e3898033c70 WorkerThread "GC Thread#28" [stack: 0x00007e3859ebf000,0x00007e3859fbf000] [id=142635]
0x00007e3898034be0 WorkerThread "GC Thread#29" [stack: 0x00007e3859dbd000,0x00007e3859ebd000] [id=142636]
0x00007e3898035b50 WorkerThread "GC Thread#30" [stack: 0x00007e3859cbb000,0x00007e3859dbb000] [id=142637]
0x00007e3898036ac0 WorkerThread "GC Thread#31" [stack: 0x00007e3859bb9000,0x00007e3859cb9000] [id=142638]
0x00007e3898037a30 WorkerThread "GC Thread#32" [stack: 0x00007e3859ab7000,0x00007e3859bb7000] [id=142639]
0x00007e38980389a0 WorkerThread "GC Thread#33" [stack: 0x00007e38599b5000,0x00007e3859ab5000] [id=142640]
0x00007e3898039910 WorkerThread "GC Thread#34" [stack: 0x00007e38598b3000,0x00007e38599b3000] [id=142641]
0x00007e389803a880 WorkerThread "GC Thread#35" [stack: 0x00007e38597b1000,0x00007e38598b1000] [id=142642]
0x00007e389803b7f0 WorkerThread "GC Thread#36" [stack: 0x00007e38596af000,0x00007e38597af000] [id=142643]
0x00007e389803c760 WorkerThread "GC Thread#37" [stack: 0x00007e38595ad000,0x00007e38596ad000] [id=142644]
0x00007e389803d6d0 WorkerThread "GC Thread#38" [stack: 0x00007e38594ab000,0x00007e38595ab000] [id=142645]
0x00007e389803e640 WorkerThread "GC Thread#39" [stack: 0x00007e38593a9000,0x00007e38594a9000] [id=142646]
0x00007e389803f5b0 WorkerThread "GC Thread#40" [stack: 0x00007e38592a7000,0x00007e38593a7000] [id=142647]
0x00007e3898040520 WorkerThread "GC Thread#41" [stack: 0x00007e38591a5000,0x00007e38592a5000] [id=142648]
0x00007e3898041490 WorkerThread "GC Thread#42" [stack: 0x00007e38590a3000,0x00007e38591a3000] [id=142649]
0x00007e3898042400 WorkerThread "GC Thread#43" [stack: 0x00007e3858fa1000,0x00007e38590a1000] [id=142650]
0x00007e3898043370 WorkerThread "GC Thread#44" [stack: 0x00007e3858e9f000,0x00007e3858f9f000] [id=142651]
0x00007e38980442e0 WorkerThread "GC Thread#45" [stack: 0x00007e3858d9d000,0x00007e3858e9d000] [id=142652]
0x00007e3898045250 WorkerThread "GC Thread#46" [stack: 0x00007e3858c9b000,0x00007e3858d9b000] [id=142653]
0x00007e38980461c0 WorkerThread "GC Thread#47" [stack: 0x00007e3858b99000,0x00007e3858c99000] [id=142654]
0x00007e3898047130 WorkerThread "GC Thread#48" [stack: 0x00007e3858a97000,0x00007e3858b97000] [id=142655]
0x00007f084c0a8b70 ConcurrentGCThread "G1 Main Marker" [stack: 0x00007e38bdd54000,0x00007e38bde54000] [id=141618]
0x00007f084c0a9c50 WorkerThread "G1 Conc#0" [stack: 0x00007e38bdc52000,0x00007e38bdd52000] [id=141619]
0x00007e38b0000960 WorkerThread "G1 Conc#1" [stack: 0x00007e3858995000,0x00007e3858a95000] [id=142757]
0x00007e38b00011e0 WorkerThread "G1 Conc#2" [stack: 0x00007e38587a1000,0x00007e38588a1000] [id=142758]
0x00007e38b0001ba0 WorkerThread "G1 Conc#3" [stack: 0x00007e385869f000,0x00007e385879f000] [id=142759]
0x00007e38b0002720 WorkerThread "G1 Conc#4" [stack: 0x00007e385859d000,0x00007e385869d000] [id=142760]
0x00007e38b00032a0 WorkerThread "G1 Conc#5" [stack: 0x00007e385849b000,0x00007e385859b000] [id=142761]
0x00007e38b0003e20 WorkerThread "G1 Conc#6" [stack: 0x00007e3858399000,0x00007e3858499000] [id=142762]
0x00007e38b00049a0 WorkerThread "G1 Conc#7" [stack: 0x00007e3858297000,0x00007e3858397000] [id=142763]
0x00007e38b0005910 WorkerThread "G1 Conc#8" [stack: 0x00007e3858195000,0x00007e3858295000] [id=142764]
0x00007e38b0006880 WorkerThread "G1 Conc#9" [stack: 0x00007e3858093000,0x00007e3858193000] [id=142765]
0x00007e38b00077f0 WorkerThread "G1 Conc#10" [stack: 0x00007e376ff00000,0x00007e3770000000] [id=142766]
0x00007e38b0008760 WorkerThread "G1 Conc#11" [stack: 0x00007e376fdfe000,0x00007e376fefe000] [id=142767]
0x00007e38b00096d0 WorkerThread "G1 Conc#12" [stack: 0x00007e376fcfc000,0x00007e376fdfc000] [id=142768]
0x00007e38b000a640 WorkerThread "G1 Conc#13" [stack: 0x00007e376fbfa000,0x00007e376fcfa000] [id=142769]
0x00007e38b000b5b0 WorkerThread "G1 Conc#14" [stack: 0x00007e376faf8000,0x00007e376fbf8000] [id=142770]
0x00007e38b000c520 WorkerThread "G1 Conc#15" [stack: 0x00007e376f9f6000,0x00007e376faf6000] [id=142771]
0x00007e38b000d490 WorkerThread "G1 Conc#16" [stack: 0x00007e376f8f4000,0x00007e376f9f4000] [id=142772]
0x00007e38b000e400 WorkerThread "G1 Conc#17" [stack: 0x00007e376f7f2000,0x00007e376f8f2000] [id=142773]
0x00007e38b000f370 WorkerThread "G1 Conc#18" [stack: 0x00007e376f6f0000,0x00007e376f7f0000] [id=142774]
0x00007e38b00102e0 WorkerThread "G1 Conc#19" [stack: 0x00007e376f5ee000,0x00007e376f6ee000] [id=142775]
0x00007e38b0011250 WorkerThread "G1 Conc#20" [stack: 0x00007e376f4ec000,0x00007e376f5ec000] [id=142776]
0x00007e38b00121c0 WorkerThread "G1 Conc#21" [stack: 0x00007e376f3ea000,0x00007e376f4ea000] [id=142777]
0x00007e38b0013130 WorkerThread "G1 Conc#22" [stack: 0x00007e376f2e8000,0x00007e376f3e8000] [id=142778]
0x00007e38b00140a0 WorkerThread "G1 Conc#23" [stack: 0x00007e376f1e6000,0x00007e376f2e6000] [id=142779]
0x00007e38b0015010 WorkerThread "G1 Conc#24" [stack: 0x00007e376f0e4000,0x00007e376f1e4000] [id=142780]
0x00007e38b0015f80 WorkerThread "G1 Conc#25" [stack: 0x00007e376efe2000,0x00007e376f0e2000] [id=142781]
0x00007f084c279310 ConcurrentGCThread "G1 Refine#0" [stack: 0x00007e38a93b5000,0x00007e38a94b5000] [id=141620]
0x00007f084c27a300 ConcurrentGCThread "G1 Service" [stack: 0x00007e38a92b3000,0x00007e38a93b3000] [id=141621]
Threads with active compile tasks:
VM state: not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
CDS archive(s) mapped at: [0x0000000800000000-0x0000000800b8c000-0x0000000800b8c000), size 12107776, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 0.
Compressed class space mapped at: 0x0000000800c00000-0x0000000840c00000, reserved size: 1073741824
Narrow klass base: 0x0000000800000000, Narrow klass shift: 0, Narrow klass range: 0x100000000
GC Precious Log:
CardTable entry size: 512
Card Set container configuration: InlinePtr #cards 3 size 8 Array Of Cards #cards 256 size 528 Howl #buckets 8 coarsen threshold 58982 Howl Bitmap #cards 8192 size 1040 coarsen threshold 7372 Card regions per heap region 1 cards per card region 65536
CPUs: 160 total, 160 available
Memory: 2015G
Large Page Support: Disabled
NUMA Support: Disabled
Compressed Oops: Disabled
Heap Region Size: 32M
Heap Min Capacity: 32M
Heap Initial Capacity: 2G
Heap Max Capacity: 800G
Pre-touch: Disabled
Parallel Workers: 103
Concurrent Workers: 26
Concurrent Refinement Workers: 103
Periodic GC: Disabled
Heap:
garbage-first heap total 1474560K, used 144015K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 4 young (131072K), 1 survivors (32768K)
Metaspace used 46240K, committed 46656K, reserved 1114112K
class space used 5871K, committed 6080K, reserved 1048576K
Heap Regions: E=young(eden), S=young(survivor), O=old, HS=humongous(starts), HC=humongous(continues), CS=collection set, F=free, OA=open archive, CA=closed archive, TAMS=top-at-mark-start (previous, next)
| 0|0x00007e4030000000, 0x00007e4030fe9000, 0x00007e4032000000| 49%| O| |TAMS 0x00007e4030000000, 0x00007e4030000000| Untracked
| 1|0x00007e4032000000, 0x00007e4032000000, 0x00007e4034000000| 0%| F| |TAMS 0x00007e4032000000, 0x00007e4032000000| Untracked
| 2|0x00007e4034000000, 0x00007e4036000000, 0x00007e4036000000|100%| O| |TAMS 0x00007e4034449600, 0x00007e4034000000| Untracked
| 3|0x00007e4036000000, 0x00007e4036000000, 0x00007e4038000000| 0%| F| |TAMS 0x00007e4036000000, 0x00007e4036000000| Untracked
| 4|0x00007e4038000000, 0x00007e4038000000, 0x00007e403a000000| 0%| F| |TAMS 0x00007e4038000000, 0x00007e4038000000| Untracked
| 5|0x00007e403a000000, 0x00007e403a000000, 0x00007e403c000000| 0%| F| |TAMS 0x00007e403a000000, 0x00007e403a000000| Untracked
| 6|0x00007e403c000000, 0x00007e403c000000, 0x00007e403e000000| 0%| F| |TAMS 0x00007e403c000000, 0x00007e403c000000| Untracked
| 7|0x00007e403e000000, 0x00007e403e000000, 0x00007e4040000000| 0%| F| |TAMS 0x00007e403e000000, 0x00007e403e000000| Untracked
| 8|0x00007e4040000000, 0x00007e4040000000, 0x00007e4042000000| 0%| F| |TAMS 0x00007e4040000000, 0x00007e4040000000| Untracked
| 9|0x00007e4042000000, 0x00007e4042000000, 0x00007e4044000000| 0%| F| |TAMS 0x00007e4042000000, 0x00007e4042000000| Untracked
| 10|0x00007e4044000000, 0x00007e4044000000, 0x00007e4046000000| 0%| F| |TAMS 0x00007e4044000000, 0x00007e4044000000| Untracked
| 11|0x00007e4046000000, 0x00007e4046000000, 0x00007e4048000000| 0%| F| |TAMS 0x00007e4046000000, 0x00007e4046000000| Untracked
| 12|0x00007e4048000000, 0x00007e4048000000, 0x00007e404a000000| 0%| F| |TAMS 0x00007e4048000000, 0x00007e4048000000| Untracked
| 13|0x00007e404a000000, 0x00007e404a000000, 0x00007e404c000000| 0%| F| |TAMS 0x00007e404a000000, 0x00007e404a000000| Untracked
| 14|0x00007e404c000000, 0x00007e404c000000, 0x00007e404e000000| 0%| F| |TAMS 0x00007e404c000000, 0x00007e404c000000| Untracked
| 15|0x00007e404e000000, 0x00007e404fcbaea8, 0x00007e4050000000| 89%| S|CS|TAMS 0x00007e404e000000, 0x00007e404e000000| Complete
| 16|0x00007e4050000000, 0x00007e4050000000, 0x00007e4052000000| 0%| F| |TAMS 0x00007e4050000000, 0x00007e4050000000| Untracked
| 17|0x00007e4052000000, 0x00007e4052000000, 0x00007e4054000000| 0%| F| |TAMS 0x00007e4052000000, 0x00007e4052000000| Untracked
| 18|0x00007e4054000000, 0x00007e4054000000, 0x00007e4056000000| 0%| F| |TAMS 0x00007e4054000000, 0x00007e4054000000| Untracked
| 19|0x00007e4056000000, 0x00007e4056000000, 0x00007e4058000000| 0%| F| |TAMS 0x00007e4056000000, 0x00007e4056000000| Untracked
| 20|0x00007e4058000000, 0x00007e4058000000, 0x00007e405a000000| 0%| F| |TAMS 0x00007e4058000000, 0x00007e4058000000| Untracked
| 21|0x00007e405a000000, 0x00007e405a000000, 0x00007e405c000000| 0%| F| |TAMS 0x00007e405a000000, 0x00007e405a000000| Untracked
| 22|0x00007e405c000000, 0x00007e405c000000, 0x00007e405e000000| 0%| F| |TAMS 0x00007e405c000000, 0x00007e405c000000| Untracked
| 23|0x00007e405e000000, 0x00007e405e000000, 0x00007e4060000000| 0%| F| |TAMS 0x00007e405e000000, 0x00007e405e000000| Untracked
| 24|0x00007e4060000000, 0x00007e4060000000, 0x00007e4062000000| 0%| F| |TAMS 0x00007e4060000000, 0x00007e4060000000| Untracked
| 25|0x00007e4062000000, 0x00007e4062000000, 0x00007e4064000000| 0%| F| |TAMS 0x00007e4062000000, 0x00007e4062000000| Untracked
| 26|0x00007e4064000000, 0x00007e4064000000, 0x00007e4066000000| 0%| F| |TAMS 0x00007e4064000000, 0x00007e4064000000| Untracked
| 27|0x00007e4066000000, 0x00007e4066000000, 0x00007e4068000000| 0%| F| |TAMS 0x00007e4066000000, 0x00007e4066000000| Untracked
| 28|0x00007e4068000000, 0x00007e4068000000, 0x00007e406a000000| 0%| F| |TAMS 0x00007e4068000000, 0x00007e4068000000| Untracked
| 29|0x00007e406a000000, 0x00007e406a000000, 0x00007e406c000000| 0%| F| |TAMS 0x00007e406a000000, 0x00007e406a000000| Untracked
| 30|0x00007e406c000000, 0x00007e406c000000, 0x00007e406e000000| 0%| F| |TAMS 0x00007e406c000000, 0x00007e406c000000| Untracked
| 31|0x00007e406e000000, 0x00007e406e000000, 0x00007e4070000000| 0%| F| |TAMS 0x00007e406e000000, 0x00007e406e000000| Untracked
| 32|0x00007e4070000000, 0x00007e4070000000, 0x00007e4072000000| 0%| F| |TAMS 0x00007e4070000000, 0x00007e4070000000| Untracked
| 33|0x00007e4072000000, 0x00007e4072000000, 0x00007e4074000000| 0%| F| |TAMS 0x00007e4072000000, 0x00007e4072000000| Untracked
| 34|0x00007e4074000000, 0x00007e4074000000, 0x00007e4076000000| 0%| F| |TAMS 0x00007e4074000000, 0x00007e4074000000| Untracked
| 35|0x00007e4076000000, 0x00007e4076000000, 0x00007e4078000000| 0%| F| |TAMS 0x00007e4076000000, 0x00007e4076000000| Untracked
| 36|0x00007e4078000000, 0x00007e4078000000, 0x00007e407a000000| 0%| F| |TAMS 0x00007e4078000000, 0x00007e4078000000| Untracked
| 37|0x00007e407a000000, 0x00007e407a000000, 0x00007e407c000000| 0%| F| |TAMS 0x00007e407a000000, 0x00007e407a000000| Untracked
| 38|0x00007e407c000000, 0x00007e407c000000, 0x00007e407e000000| 0%| F| |TAMS 0x00007e407c000000, 0x00007e407c000000| Untracked
| 39|0x00007e407e000000, 0x00007e407e000000, 0x00007e4080000000| 0%| F| |TAMS 0x00007e407e000000, 0x00007e407e000000| Untracked
| 40|0x00007e4080000000, 0x00007e4080000000, 0x00007e4082000000| 0%| F| |TAMS 0x00007e4080000000, 0x00007e4080000000| Untracked
| 41|0x00007e4082000000, 0x00007e4082000000, 0x00007e4084000000| 0%| F| |TAMS 0x00007e4082000000, 0x00007e4082000000| Untracked
| 42|0x00007e4084000000, 0x00007e4084d553d8, 0x00007e4086000000| 41%| E| |TAMS 0x00007e4084000000, 0x00007e4084000000| Complete
| 62|0x00007e40ac000000, 0x00007e40ae000000, 0x00007e40ae000000|100%| E|CS|TAMS 0x00007e40ac000000, 0x00007e40ac000000| Complete
| 63|0x00007e40ae000000, 0x00007e40b0000000, 0x00007e40b0000000|100%| E|CS|TAMS 0x00007e40ae000000, 0x00007e40ae000000| Complete
Card table byte_map: [0x00007e3f666ff000,0x00007e3fca6ff000] _byte_map_base: 0x00007e004657f000
Marking Bits (Prev, Next): (CMBitMap*) 0x00007f084c0a7d10, (CMBitMap*) 0x00007f084c0a7d50
Prev Bits: [0x00007e3be26ff000, 0x00007e3f026ff000)
Next Bits: [0x00007e38c26ff000, 0x00007e3be26ff000)
Polling page: 0x00007f0855e75000
Metaspace:
Usage:
Non-class: 39.42 MB used.
Class: 5.73 MB used.
Both: 45.16 MB used.
Virtual space:
Non-class space: 64.00 MB reserved, 39.62 MB ( 62%) committed, 1 nodes.
Class space: 1.00 GB reserved, 5.94 MB ( <1%) committed, 1 nodes.
Both: 1.06 GB reserved, 45.56 MB ( 4%) committed.
Chunk freelists:
Non-Class: 3.64 MB
Class: 2.05 MB
Both: 5.69 MB
MaxMetaspaceSize: unlimited
CompressedClassSpaceSize: 1.00 GB
Initial GC threshold: 21.00 MB
Current GC threshold: 59.19 MB
CDS: on
MetaspaceReclaimPolicy: balanced
- commit_granule_bytes: 65536.
- commit_granule_words: 8192.
- virtual_space_node_default_size: 8388608.
- enlarge_chunks_in_place: 1.
- new_chunks_are_fully_committed: 0.
- uncommit_free_chunks: 1.
- use_allocation_guard: 0.
Internal statistics:
num_allocs_failed_limit: 6.
num_arena_births: 514.
num_arena_deaths: 0.
num_vsnodes_births: 2.
num_vsnodes_deaths: 0.
num_space_committed: 728.
num_space_uncommitted: 0.
num_chunks_returned_to_freelist: 6.
num_chunks_taken_from_freelist: 1929.
num_chunk_merges: 6.
num_chunk_splits: 1504.
num_chunks_enlarged: 1254.
num_inconsistent_stats: 0.
CodeHeap 'non-profiled nmethods': size=118304Kb used=4656Kb max_used=4656Kb free=113647Kb
bounds [0x00007f083ce8a000, 0x00007f083d31a000, 0x00007f0844212000]
CodeHeap 'profiled nmethods': size=118300Kb used=10073Kb max_used=10073Kb free=108226Kb
bounds [0x00007f0835b03000, 0x00007f08364e3000, 0x00007f083ce8a000]
CodeHeap 'non-nmethods': size=9156Kb used=4725Kb max_used=4820Kb free=4430Kb
bounds [0x00007f0835212000, 0x00007f0835732000, 0x00007f0835b03000]
total_blobs=6108 nmethods=5443 adapters=571
compilation: enabled
stopped_count=0, restarted_count=0
full_count=0
Compilation events (20 events):
Event: 11.439 Thread 0x00007e38780653b0 6420 1 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet::setRegionForGenotyping (6 bytes)
Event: 11.439 Thread 0x00007e3878039ed0 6421 1 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet::setFullReferenceWithPadding (6 bytes)
Event: 11.439 Thread 0x00007e38780d05a0 6422 1 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet::setPaddedReferenceLoc (6 bytes)
Event: 11.439 Thread 0x00007e38780d05a0 nmethod 6422 0x00007f083d30b210 code [0x00007f083d30b3a0, 0x00007f083d30b4b0]
Event: 11.439 Thread 0x00007e38780653b0 nmethod 6420 0x00007f083d30b510 code [0x00007f083d30b6a0, 0x00007f083d30b7b0]
Event: 11.439 Thread 0x00007e3878039ed0 nmethod 6421 0x00007f083d30b810 code [0x00007f083d30b9a0, 0x00007f083d30bab0]
Event: 11.442 Thread 0x00007e38741b5e50 nmethod 6393 0x00007f083d30bb10 code [0x00007f083d30bce0, 0x00007f083d30ce78]
Event: 11.548 Thread 0x00007e38741b7150 nmethod 6386 0x00007f083d30d810 code [0x00007f083d30dca0, 0x00007f083d312c00]
Event: 11.579 Thread 0x00007e3860102c30 6423 3 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph$$Lambda$321/0x00000008011b4dc0::apply (8 bytes)
Event: 11.579 Thread 0x00007f084c2c9b20 6424 3 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph::lambda$addSequence$1 (8 bytes)
Event: 11.579 Thread 0x00007e3878038ed0 6425 3 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph$$Lambda$322/0x00000008011b4fe8::apply (8 bytes)
Event: 11.579 Thread 0x00007e3870027250 6426 3 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph::lambda$getAllPendingSequences$0 (7 bytes)
Event: 11.579 Thread 0x00007f084c2c9b20 nmethod 6424 0x00007f08364d8a90 code [0x00007f08364d8c60, 0x00007f08364d8f90]
Event: 11.579 Thread 0x00007e3860102c30 nmethod 6423 0x00007f08364d9110 code [0x00007f08364d92e0, 0x00007f08364d9770]
Event: 11.580 Thread 0x00007e3870027250 nmethod 6426 0x00007f08364d9910 code [0x00007f08364d9ac0, 0x00007f08364d9c60]
Event: 11.580 Thread 0x00007e3878038ed0 nmethod 6425 0x00007f08364d9d10 code [0x00007f08364d9ec0, 0x00007f08364da200]
Event: 11.715 Thread 0x00007f084c2c84a0 6427 4 java.lang.AbstractStringBuilder::append (54 bytes)
Event: 11.726 Thread 0x00007f084c2c84a0 nmethod 6427 0x00007f083d315110 code [0x00007f083d3152e0, 0x00007f083d315c08]
Event: 11.764 Thread 0x00007e38780d05a0 6428 1 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet::getRegionForGenotyping (5 bytes)
Event: 11.764 Thread 0x00007e38780d05a0 nmethod 6428 0x00007f083d316090 code [0x00007f083d316220, 0x00007f083d3162f0]
GC Heap History (20 events):
Event: 4.139 GC heap before
{Heap before GC invocations=4 (full 0):
garbage-first heap total 327680K, used 57149K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 2 young (65536K), 1 survivors (32768K)
Metaspace used 32192K, committed 32448K, reserved 1114112K
class space used 4356K, committed 4480K, reserved 1048576K
}
Event: 4.158 GC heap after
{Heap after GC invocations=5 (full 0):
garbage-first heap total 327680K, used 39755K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 32192K, committed 32448K, reserved 1114112K
class space used 4356K, committed 4480K, reserved 1048576K
}
Event: 4.693 GC heap before
{Heap before GC invocations=5 (full 0):
garbage-first heap total 327680K, used 138059K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 5 young (163840K), 1 survivors (32768K)
Metaspace used 36085K, committed 36288K, reserved 1114112K
class space used 4867K, committed 4992K, reserved 1048576K
}
Event: 4.701 GC heap after
{Heap after GC invocations=6 (full 0):
garbage-first heap total 327680K, used 40812K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 36085K, committed 36288K, reserved 1114112K
class space used 4867K, committed 4992K, reserved 1048576K
}
Event: 5.767 GC heap before
{Heap before GC invocations=7 (full 0):
garbage-first heap total 327680K, used 171884K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 5 young (163840K), 1 survivors (32768K)
Metaspace used 41214K, committed 41472K, reserved 1114112K
class space used 5398K, committed 5568K, reserved 1048576K
}
Event: 5.775 GC heap after
{Heap after GC invocations=8 (full 0):
garbage-first heap total 327680K, used 46335K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 41214K, committed 41472K, reserved 1114112K
class space used 5398K, committed 5568K, reserved 1048576K
}
Event: 5.789 GC heap before
{Heap before GC invocations=8 (full 0):
garbage-first heap total 327680K, used 79103K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 2 young (65536K), 1 survivors (32768K)
Metaspace used 41219K, committed 41536K, reserved 1114112K
class space used 5398K, committed 5568K, reserved 1048576K
}
Event: 5.820 GC heap after
{Heap after GC invocations=9 (full 0):
garbage-first heap total 327680K, used 58614K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 41219K, committed 41536K, reserved 1114112K
class space used 5398K, committed 5568K, reserved 1048576K
}
Event: 6.727 GC heap before
{Heap before GC invocations=9 (full 0):
garbage-first heap total 327680K, used 189686K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 5 young (163840K), 1 survivors (32768K)
Metaspace used 43154K, committed 43456K, reserved 1114112K
class space used 5558K, committed 5696K, reserved 1048576K
}
Event: 6.741 GC heap after
{Heap after GC invocations=10 (full 0):
garbage-first heap total 1212416K, used 71307K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 43154K, committed 43456K, reserved 1114112K
class space used 5558K, committed 5696K, reserved 1048576K
}
Event: 8.634 GC heap before
{Heap before GC invocations=10 (full 0):
garbage-first heap total 1212416K, used 726667K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 22 young (720896K), 1 survivors (32768K)
Metaspace used 45585K, committed 46016K, reserved 1114112K
class space used 5865K, committed 6080K, reserved 1048576K
}
Event: 8.645 GC heap after
{Heap after GC invocations=11 (full 0):
garbage-first heap total 1212416K, used 73242K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 45585K, committed 46016K, reserved 1114112K
class space used 5865K, committed 6080K, reserved 1048576K
}
Event: 9.460 GC heap before
{Heap before GC invocations=11 (full 0):
garbage-first heap total 1212416K, used 761370K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 22 young (720896K), 1 survivors (32768K)
Metaspace used 45802K, committed 46272K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 9.472 GC heap after
{Heap after GC invocations=12 (full 0):
garbage-first heap total 1212416K, used 74445K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 45802K, committed 46272K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 10.199 GC heap before
{Heap before GC invocations=12 (full 0):
garbage-first heap total 1212416K, used 762573K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 22 young (720896K), 1 survivors (32768K)
Metaspace used 46023K, committed 46464K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 10.209 GC heap after
{Heap after GC invocations=13 (full 0):
garbage-first heap total 1212416K, used 73762K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 46023K, committed 46464K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 10.869 GC heap before
{Heap before GC invocations=13 (full 0):
garbage-first heap total 1212416K, used 761890K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 22 young (720896K), 1 survivors (32768K)
Metaspace used 46187K, committed 46656K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 10.881 GC heap after
{Heap after GC invocations=14 (full 0):
garbage-first heap total 1212416K, used 76911K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 46187K, committed 46656K, reserved 1114112K
class space used 5870K, committed 6080K, reserved 1048576K
}
Event: 11.739 GC heap before
{Heap before GC invocations=14 (full 0):
garbage-first heap total 1212416K, used 765039K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 22 young (720896K), 1 survivors (32768K)
Metaspace used 46240K, committed 46656K, reserved 1114112K
class space used 5871K, committed 6080K, reserved 1048576K
}
Event: 11.750 GC heap after
{Heap after GC invocations=15 (full 0):
garbage-first heap total 1474560K, used 78479K [0x00007e4030000000, 0x00007f0830000000)
region size 32768K, 1 young (32768K), 1 survivors (32768K)
Metaspace used 46240K, committed 46656K, reserved 1114112K
class space used 5871K, committed 6080K, reserved 1048576K
}
Deoptimization events (20 events):
Event: 11.310 Thread 0x00007f084c014f20 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f083d05b79c relative=0x00000000000002dc
Event: 11.310 Thread 0x00007f084c014f20 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f083d05b79c method=org.broadinstitute.hellbender.utils.pileup.PileupElement.isNextToSoftClip()Z @ 4 c2
Event: 11.310 Thread 0x00007f084c014f20 DEOPT PACKING pc=0x00007f083d05b79c sp=0x00007f0855e38050
Event: 11.310 Thread 0x00007f084c014f20 DEOPT UNPACKING pc=0x00007f0835267899 sp=0x00007f0855e37fd0 mode 2
Event: 11.329 Thread 0x00007f084c014f20 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f083d208ebc relative=0x00000000000029fc
Event: 11.329 Thread 0x00007f084c014f20 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f083d208ebc method=org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.isActive(Lorg/broadinstitute/hellbender/engine/AlignmentContext;Lorg/broadinstitute/hellben
Event: 11.329 Thread 0x00007f084c014f20 DEOPT PACKING pc=0x00007f083d208ebc sp=0x00007f0855e38240
Event: 11.329 Thread 0x00007f084c014f20 DEOPT UNPACKING pc=0x00007f0835267899 sp=0x00007f0855e381f0 mode 2
Event: 11.329 Thread 0x00007f084c014f20 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f083d1ef370 relative=0x00000000000012b0
Event: 11.329 Thread 0x00007f084c014f20 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f083d1ef370 method=java.lang.Enum.equals(Ljava/lang/Object;)Z @ 2 c2
Event: 11.329 Thread 0x00007f084c014f20 DEOPT PACKING pc=0x00007f083d1ef370 sp=0x00007f0855e38260
Event: 11.329 Thread 0x00007f084c014f20 DEOPT UNPACKING pc=0x00007f0835267899 sp=0x00007f0855e380b8 mode 2
Event: 11.370 Thread 0x00007f084c014f20 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f083d1ed1b0 relative=0x0000000000000f90
Event: 11.370 Thread 0x00007f084c014f20 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f083d1ed1b0 method=java.lang.Enum.equals(Ljava/lang/Object;)Z @ 2 c2
Event: 11.370 Thread 0x00007f084c014f20 DEOPT PACKING pc=0x00007f083d1ed1b0 sp=0x00007f0855e38180
Event: 11.370 Thread 0x00007f084c014f20 DEOPT UNPACKING pc=0x00007f0835267899 sp=0x00007f0855e38060 mode 2
Event: 11.376 Thread 0x00007f084c014f20 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f083d1df5f4 relative=0x00000000000000d4
Event: 11.376 Thread 0x00007f084c014f20 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f083d1df5f4 method=java.lang.Enum.equals(Ljava/lang/Object;)Z @ 2 c2
Event: 11.376 Thread 0x00007f084c014f20 DEOPT PACKING pc=0x00007f083d1df5f4 sp=0x00007f0855e380e0
Event: 11.376 Thread 0x00007f084c014f20 DEOPT UNPACKING pc=0x00007f0835267899 sp=0x00007f0855e38000 mode 2
Classes loaded (20 events):
Event: 7.077 Loading class java/util/stream/ReduceOps$CountingSink$OfRef
Event: 7.077 Loading class java/util/stream/ReduceOps$CountingSink
Event: 7.077 Loading class java/util/stream/ReduceOps$CountingSink done
Event: 7.077 Loading class java/util/stream/ReduceOps$CountingSink$OfRef done
Event: 7.390 Loading class java/util/stream/Streams$ConcatSpliterator$OfRef
Event: 7.390 Loading class java/util/stream/Streams$ConcatSpliterator
Event: 7.390 Loading class java/util/stream/Streams$ConcatSpliterator done
Event: 7.390 Loading class java/util/stream/Streams$ConcatSpliterator$OfRef done
Event: 7.391 Loading class java/util/stream/Streams$2
Event: 7.391 Loading class java/util/stream/Streams$2 done
Event: 7.394 Loading class java/util/stream/MatchOps$2MatchSink
Event: 7.394 Loading class java/util/stream/MatchOps$2MatchSink done
Event: 7.396 Loading class java/util/stream/IntPipeline$7
Event: 7.396 Loading class java/util/stream/IntPipeline$7 done
Event: 7.396 Loading class java/util/stream/IntPipeline$7$1
Event: 7.396 Loading class java/util/stream/IntPipeline$7$1 done
Event: 7.425 Loading class java/util/TreeMap$ValueSpliterator
Event: 7.425 Loading class java/util/TreeMap$ValueSpliterator done
Event: 9.152 Loading class java/util/PriorityQueue$PriorityQueueSpliterator
Event: 9.152 Loading class java/util/PriorityQueue$PriorityQueueSpliterator done
Classes unloaded (0 events):
No events
Classes redefined (0 events):
No events
Internal exceptions (20 events):
Event: 6.951 Thread 0x00007f084c014f20 Exception <a 'java/lang/IncompatibleClassChangeError'{0x00007e40ac4f3038}: Found class java.lang.Object, but interface was expected> (0x00007e40ac4f3038)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 833]
Event: 6.981 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40ac7745d0}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, int, double)'> (0x00007e40ac7745d0)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 6.982 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40ac786ed0}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(java.lang.Object, java.lang.Object, int, java.lang.Object, java.lang.Object)'> (0x00007e40ac786ed0)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 6.985 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40ac7a2b48}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, int, java.lang.Object, java.lang.Object)'> (0x00007e40ac7a2b48)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 6.986 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40ac7ba910}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeInterface(java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00007e40ac7ba910)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.070 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40acd57638}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(java.lang.Object, java.lang.Object, double)'> (0x00007e40acd57638)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.071 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40acd5c7b8}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, double)'> (0x00007e40acd5c7b8)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.074 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40acd89a88}: 'double java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object)'> (0x00007e40acd89a88)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.392 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701912c0}: 'int java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, int)'> (0x00007e40701912c0)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.393 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701992b8}: 'int java.lang.invoke.DirectMethodHandle$Holder.invokeInterface(java.lang.Object, java.lang.Object, int)'> (0x00007e40701992b8)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.397 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701ab418}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeInterface(java.lang.Object, java.lang.Object, int)'> (0x00007e40701ab418)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.397 Thread 0x00007f084c014f20 Exception <a 'java/lang/IncompatibleClassChangeError'{0x00007e40701afa10}: Found class java.lang.Object, but interface was expected> (0x00007e40701afa10)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 833]
Event: 7.398 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701bc7f8}: 'double java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, int)'> (0x00007e40701bc7f8)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.399 Thread 0x00007f084c014f20 Implicit null exception at 0x00007f083d106604 to 0x00007f083d10703c
Event: 7.401 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701d5b50}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, long, java.lang.Object)'> (0x00007e40701d5b50)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.403 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40701f6520}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00007e40701f6520)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.422 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40702a7578}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.newInvokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00007e40702a7578)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.422 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40702adc30}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00007e40702adc30)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.423 Thread 0x00007f084c014f20 Exception <a 'java/lang/NoSuchMethodError'{0x00007e40702b2ee0}: 'java.lang.Object java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00007e40702b2ee0)
thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 766]
Event: 7.428 Thread 0x00007f084c014f20 Implicit null exception at 0x00007f083d121624 to 0x00007f083d121a7c
VM Operations (20 events):
Event: 8.050 Executing VM operation: HandshakeAllThreads
Event: 8.051 Executing VM operation: HandshakeAllThreads done
Event: 8.062 Executing VM operation: HandshakeAllThreads
Event: 8.062 Executing VM operation: HandshakeAllThreads done
Event: 8.422 Executing VM operation: ICBufferFull
Event: 8.423 Executing VM operation: ICBufferFull done
Event: 8.634 Executing VM operation: G1CollectForAllocation
Event: 8.645 Executing VM operation: G1CollectForAllocation done
Event: 9.429 Executing VM operation: ICBufferFull
Event: 9.429 Executing VM operation: ICBufferFull done
Event: 9.459 Executing VM operation: G1CollectForAllocation
Event: 9.472 Executing VM operation: G1CollectForAllocation done
Event: 10.199 Executing VM operation: G1CollectForAllocation
Event: 10.209 Executing VM operation: G1CollectForAllocation done
Event: 10.721 Executing VM operation: HandshakeAllThreads
Event: 10.721 Executing VM operation: HandshakeAllThreads done
Event: 10.869 Executing VM operation: G1CollectForAllocation
Event: 10.881 Executing VM operation: G1CollectForAllocation done
Event: 11.739 Executing VM operation: G1CollectForAllocation
Event: 11.750 Executing VM operation: G1CollectForAllocation done
Events (20 events):
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836334590
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836340a10
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836346f10
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836348790
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f083634dc10
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f083634e090
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836354890
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f0836355010
Event: 8.074 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f083638ba90
Event: 9.542 Thread 0x00007e37100053a0 Thread exited: 0x00007e37100053a0
Event: 9.547 Thread 0x00007e3710004180 Thread exited: 0x00007e3710004180
Event: 9.777 Thread 0x00007e3710002f50 Thread exited: 0x00007e3710002f50
Event: 10.360 Thread 0x00007e3710001c70 Thread exited: 0x00007e3710001c70
Event: 10.723 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f083d0bc690
Event: 10.732 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f08360bb610
Event: 10.733 Thread 0x00007f084c2cb0a0 flushing nmethod 0x00007f08361c2a90
Event: 10.919 Thread 0x00007e38741b2820 Thread exited: 0x00007e38741b2820
Event: 11.716 Thread 0x00007e38741b7150 Thread exited: 0x00007e38741b7150
Event: 11.764 Thread 0x00007e38741b5e50 Thread exited: 0x00007e38741b5e50
Event: 11.814 Protecting memory [0x00007f0855d39000,0x00007f0855d3a000] with protection modes 3
Dynamic libraries:
800000000-80043b000 rw-p 00001000 fd:00 24384258 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/classes_nocoops.jsa
80043b000-800b8c000 r--p 0043c000 fd:00 24384258 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/classes_nocoops.jsa
800b8c000-800c00000 ---p 00000000 00:00 0
800c00000-800c40000 rw-p 00000000 00:00 0
800c40000-800c80000 rw-p 00000000 00:00 0
800c80000-800ce0000 rw-p 00000000 00:00 0
800ce0000-800d00000 rw-p 00000000 00:00 0
800d00000-800d40000 rw-p 00000000 00:00 0
800d40000-801130000 rw-p 00000000 00:00 0
801130000-801140000 ---p 00000000 00:00 0
801140000-801200000 rw-p 00000000 00:00 0
801200000-840c00000 ---p 00000000 00:00 0
55d5eec34000-55d5eec35000 r-xp 00000000 fd:00 22290803 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/bin/java
55d5eee35000-55d5eee36000 r--p 00001000 fd:00 22290803 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/bin/java
55d5eee36000-55d5eee37000 rw-p 00002000 fd:00 22290803 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/bin/java
55d5f012a000-55d5f0171000 rw-p 00000000 00:00 0 [heap]
7e3700000000-7e37009a6000 rw-p 00000000 00:00 0
7e37009a6000-7e3704000000 ---p 00000000 00:00 0
7e3704000000-7e3704021000 rw-p 00000000 00:00 0
7e3704021000-7e3708000000 ---p 00000000 00:00 0
7e3708000000-7e3708c38000 rw-p 00000000 00:00 0
7e3708c38000-7e370c000000 ---p 00000000 00:00 0
7e370c000000-7e370c9d8000 rw-p 00000000 00:00 0
7e370c9d8000-7e3710000000 ---p 00000000 00:00 0
7e3710000000-7e3710961000 rw-p 00000000 00:00 0
7e3710961000-7e3714000000 ---p 00000000 00:00 0
7e3714000000-7e3714968000 rw-p 00000000 00:00 0
7e3714968000-7e3718000000 ---p 00000000 00:00 0
7e3718000000-7e3718a3d000 rw-p 00000000 00:00 0
7e3718a3d000-7e371c000000 ---p 00000000 00:00 0
7e371c000000-7e371ce91000 rw-p 00000000 00:00 0
7e371ce91000-7e3720000000 ---p 00000000 00:00 0
7e3720000000-7e372003e000 rw-p 00000000 00:00 0
7e372003e000-7e3724000000 ---p 00000000 00:00 0
7e3724000000-7e37240e6000 rw-p 00000000 00:00 0
7e37240e6000-7e3728000000 ---p 00000000 00:00 0
7e3728000000-7e3728021000 rw-p 00000000 00:00 0
7e3728021000-7e372c000000 ---p 00000000 00:00 0
7e372c000000-7e372c0c5000 rw-p 00000000 00:00 0
7e372c0c5000-7e3730000000 ---p 00000000 00:00 0
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7e376e5db000-7e376e61d000 r-xp 00000000 fd:03 121112145 /data/nobackup/tmp/libgkl_pairhmm_omp13802390137529139622.so
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7f0853547000-7f0853548000 r--p 00100000 fd:00 19664137 /usr/lib64/libm-2.17.so
7f0853548000-7f0853549000 rw-p 00101000 fd:00 19664137 /usr/lib64/libm-2.17.so
7f0853549000-7f08536bd000 r-xp 00000000 00:47 111829157 /net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib64/libstdc++.so.6.0.25
7f08536bd000-7f08538bc000 ---p 00174000 00:47 111829157 /net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib64/libstdc++.so.6.0.25
7f08538bc000-7f08538c6000 r--p 00173000 00:47 111829157 /net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib64/libstdc++.so.6.0.25
7f08538c6000-7f08538c8000 rw-p 0017d000 00:47 111829157 /net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib64/libstdc++.so.6.0.25
7f08538c8000-7f08538cc000 rw-p 00000000 00:00 0
7f08538cc000-7f08538d3000 r-xp 00000000 fd:00 19664159 /usr/lib64/librt-2.17.so
7f08538d3000-7f0853ad2000 ---p 00007000 fd:00 19664159 /usr/lib64/librt-2.17.so
7f0853ad2000-7f0853ad3000 r--p 00006000 fd:00 19664159 /usr/lib64/librt-2.17.so
7f0853ad3000-7f0853ad4000 rw-p 00007000 fd:00 19664159 /usr/lib64/librt-2.17.so
7f0853ad4000-7f0854cf5000 r-xp 00000000 fd:00 24384264 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/libjvm.so
7f0854cf5000-7f0854ef4000 ---p 01221000 fd:00 24384264 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/libjvm.so
7f0854ef4000-7f0854fb5000 r--p 01220000 fd:00 24384264 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/libjvm.so
7f0854fb5000-7f0854fea000 rw-p 012e1000 fd:00 24384264 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/server/libjvm.so
7f0854fea000-7f0855044000 rw-p 00000000 00:00 0
7f0855044000-7f0855208000 r-xp 00000000 fd:00 19664129 /usr/lib64/libc-2.17.so
7f0855208000-7f0855407000 ---p 001c4000 fd:00 19664129 /usr/lib64/libc-2.17.so
7f0855407000-7f085540b000 r--p 001c3000 fd:00 19664129 /usr/lib64/libc-2.17.so
7f085540b000-7f085540d000 rw-p 001c7000 fd:00 19664129 /usr/lib64/libc-2.17.so
7f085540d000-7f0855412000 rw-p 00000000 00:00 0
7f0855412000-7f0855414000 r-xp 00000000 fd:00 19664135 /usr/lib64/libdl-2.17.so
7f0855414000-7f0855614000 ---p 00002000 fd:00 19664135 /usr/lib64/libdl-2.17.so
7f0855614000-7f0855615000 r--p 00002000 fd:00 19664135 /usr/lib64/libdl-2.17.so
7f0855615000-7f0855616000 rw-p 00003000 fd:00 19664135 /usr/lib64/libdl-2.17.so
7f0855616000-7f085562d000 r-xp 00000000 fd:00 19664155 /usr/lib64/libpthread-2.17.so
7f085562d000-7f085582c000 ---p 00017000 fd:00 19664155 /usr/lib64/libpthread-2.17.so
7f085582c000-7f085582d000 r--p 00016000 fd:00 19664155 /usr/lib64/libpthread-2.17.so
7f085582d000-7f085582e000 rw-p 00017000 fd:00 19664155 /usr/lib64/libpthread-2.17.so
7f085582e000-7f0855832000 rw-p 00000000 00:00 0
7f0855832000-7f0855840000 r-xp 00000000 fd:00 24384193 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/libjli.so
7f0855840000-7f0855a40000 ---p 0000e000 fd:00 24384193 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/libjli.so
7f0855a40000-7f0855a41000 r--p 0000e000 fd:00 24384193 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/libjli.so
7f0855a41000-7f0855a42000 rw-p 0000f000 fd:00 24384193 /usr/lib/jvm/java-18-openjdk-18.0.1.0.10-2.rolling.el7.x86_64/lib/libjli.so
7f0855a42000-7f0855a57000 r-xp 00000000 fd:00 19700083 /usr/lib64/libz.so.1.2.7
7f0855a57000-7f0855c56000 ---p 00015000 fd:00 19700083 /usr/lib64/libz.so.1.2.7
7f0855c56000-7f0855c57000 r--p 00014000 fd:00 19700083 /usr/lib64/libz.so.1.2.7
7f0855c57000-7f0855c58000 rw-p 00015000 fd:00 19700083 /usr/lib64/libz.so.1.2.7
7f0855c58000-7f0855c7a000 r-xp 00000000 fd:00 19664121 /usr/lib64/ld-2.17.so
7f0855ca1000-7f0855d3a000 rw-p 00000000 00:00 0
7f0855d3a000-7f0855d3d000 ---p 00000000 00:00 0
7f0855d3d000-7f0855e3f000 rw-p 00000000 00:00 0
7f0855e53000-7f0855e54000 rw-p 00000000 00:00 0
7f0855e54000-7f0855e5b000 r--s 00000000 fd:00 19923584 /usr/lib64/gconv/gconv-modules.cache
7f0855e5b000-7f0855e66000 rw-p 00000000 00:00 0
7f0855e66000-7f0855e6d000 ---p 00000000 00:00 0
7f0855e6d000-7f0855e75000 rw-s 00000000 fd:03 125895019 /data/nobackup/tmp/hsperfdata_mdnoyes/141529
7f0855e75000-7f0855e76000 ---p 00000000 00:00 0
7f0855e76000-7f0855e77000 r--p 00000000 00:00 0
7f0855e77000-7f0855e78000 ---p 00000000 00:00 0
7f0855e78000-7f0855e79000 rw-p 00000000 00:00 0
7f0855e79000-7f0855e7a000 r--p 00021000 fd:00 19664121 /usr/lib64/ld-2.17.so
7f0855e7a000-7f0855e7b000 rw-p 00022000 fd:00 19664121 /usr/lib64/ld-2.17.so
7f0855e7b000-7f0855e7c000 rw-p 00000000 00:00 0
7ffc16c38000-7ffc16c5b000 rw-p 00000000 00:00 0 [stack]
7ffc16d17000-7ffc16d19000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
VM Arguments:
jvm_args: -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx800G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true
java_command: /net/eichler/vol26/7200/software/modules-sw/gatk/4.4.0.0/Linux/CentOS7/x86_64/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller --native-pair-hmm-threads 1 --reference /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/platinum_genomes/chm13v2.0_maskedY_rCRS.fa.gz --input /net/eichler/vol28/projects/platinum_genomes/nobackups/denovo/alignment/hifi/CHM13_v2.0/K1463_2281_ccs_to_chm13.bam --output K1463.2281.chr7_part_2c.g.vcf.gz --pcr-indel-model AGGRESSIVE --intervals chr7_part_2c.bed --minimum-mapping-quality 60 --read-filter MappingQualityReadFilter --read-filter NotSecondaryAlignmentReadFilter --read-filter NotSupplementaryAlignmentReadFilter -ERC GVCF
java_class_path (initial): /net/eichler/vol26/7200/software/modules-sw/gatk/4.4.0.0/Linux/CentOS7/x86_64/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar
Launcher Type: SUN_STANDARD
[Global flags]
intx CICompilerCount = 21 {product} {ergonomic}
uint ConcGCThreads = 26 {product} {ergonomic}
uint G1ConcRefinementThreads = 103 {product} {ergonomic}
size_t G1HeapRegionSize = 33554432 {product} {ergonomic}
uintx GCDrainStackTargetSize = 64 {product} {ergonomic}
size_t InitialHeapSize = 2147483648 {product} {ergonomic}
size_t MarkStackSize = 4194304 {product} {ergonomic}
size_t MaxHeapSize = 858993459200 {product} {command line}
size_t MaxNewSize = 515396075520 {product} {ergonomic}
size_t MinHeapDeltaBytes = 33554432 {product} {ergonomic}
size_t MinHeapSize = 33554432 {product} {ergonomic}
uintx NonNMethodCodeHeapSize = 9372180 {pd product} {ergonomic}
uintx NonProfiledCodeHeapSize = 121143030 {pd product} {ergonomic}
uintx ProfiledCodeHeapSize = 121143030 {pd product} {ergonomic}
uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
bool SegmentedCodeCache = true {product} {ergonomic}
size_t SoftMaxHeapSize = 858993459200 {manageable} {ergonomic}
bool UseCompressedClassPointers = true {product lp64_product} {ergonomic}
bool UseG1GC = true {product} {ergonomic}
Logging:
Log output configuration:
#0: stdout all=warning uptime,level,tags foldmultilines=false
#1: stderr all=off uptime,level,tags foldmultilines=false
Environment Variables:
PATH=/net/eichler/vol26/7200/software/modules-sw/gatk/4.4.0.0/Linux/CentOS7/x86_64/bin:/net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/bin/:/net/gs/vol3/software/modules-sw/gsits-util/1.0/Linux/CentOS7/x86_64/misc:/net/gs/vol3/software/modules-sw/gsits-util/1.0/Linux/CentOS7/x86_64/sge:/net/eichler/vol26/home/mdnoyes/.cargo/bin:/net/eichler/vol26/7200/software/modules-sw/bcftools/1.9/Linux/CentOS7/x86_64/bin:/net/gs/vol3/software/modules-sw/htslib/1.9-20/Linux/CentOS7/x86_64/bin:/net/eichler/vol26/7200/software/modules-sw/bedtools/2.29.0/Linux/CentOS7/x86_64/bin:/net/gs/vol3/software/modules-sw/samtools/1.9/Linux/CentOS7/x86_64/bin/:/net/gs/vol3/software/modules-sw/tabix/0.2.6/Linux/CentOS7/x86_64/bin:/usr/share/Modules/bin:/opt/sge/bin/lx-amd64:/opt/sge/local:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin
LD_LIBRARY_PATH=/net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib64/:/net/gs/vol3/software/modules-sw/gcc/8.2.0/Linux/CentOS7/x86_64/lib/:/net/gs/vol3/software/modules-sw/htslib/1.9-20/Linux/CentOS7/x86_64:/net/gs/vol3/software/modules-sw/htslib/1.9-20/Linux/CentOS7/x86_64/lib:/net/gs/vol3/software/modules-sw/samtools/1.9/Linux/CentOS7/x86_64/lib/:/net/gs/vol3/software/modules-sw/tabix/0.2.6/Linux/CentOS7/x86_64/lib/
SHELL=/bin/bash
LANG=en_US.UTF-8
Signal Handlers:
SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO
SIGHUP: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGINT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGTERM: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO
--------------- S Y S T E M ---------------
OS:
CentOS Linux release 7.9.2009 (Core)
uname: Linux 3.10.0-1160.81.1.el7.x86_64 #1 SMP Fri Dec 16 17:29:43 UTC 2022 x86_64
OS uptime: 63 days 5:44 hours
libc: glibc 2.17 NPTL 2.17
rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/0k , NPROC 8192/8192 , NOFILE 12000/12000 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK 264312484k/264312484k
load average: 71.07 72.21 71.47
/proc/meminfo:
MemTotal: 2112944968 kB
MemFree: 601729932 kB
MemAvailable: 616121988 kB
Buffers: 484480 kB
Cached: 8369076 kB
SwapCached: 0 kB
Active: 1466672588 kB
Inactive: 3101956 kB
Active(anon): 1461189796 kB
Inactive(anon): 156184 kB
Active(file): 5482792 kB
Inactive(file): 2945772 kB
Unevictable: 4194304 kB
Mlocked: 4194304 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 388 kB
Writeback: 0 kB
AnonPages: 1465091012 kB
Mapped: 696724 kB
Shmem: 424992 kB
Slab: 12117360 kB
SReclaimable: 11182220 kB
SUnreclaim: 935140 kB
KernelStack: 64464 kB
PageTables: 3198692 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 1056472484 kB
Committed_AS: 1363871824 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 4066688 kB
VmallocChunk: 32476577780 kB
Percpu: 113664 kB
HardwareCorrupted: 4 kB
AnonHugePages: 688162816 kB
CmaTotal: 0 kB
CmaFree: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 786432 kB
DirectMap2M: 18585600 kB
DirectMap1G: 2129657856 kB
/sys/kernel/mm/transparent_hugepage/enabled: [always] madvise never
/sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter): [always] madvise never
Process Memory:
Virtual Size: 879054696K (peak: 879054696K)
Resident Set Size: 1241860K (peak: 1241860K) (anon: 1215056K, file: 26804K, shmem: 0K)
Swapped out: 0K
C-Heap outstanding allocations: 54408K
/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 16506709
/proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 65530
/proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 393216
container (cgroup) information:
container_type: cgroupv1
cpu_cpuset_cpus: 0-159
cpu_memory_nodes: 0-7
active_processor_count: 160
cpu_quota: no quota
cpu_period: 100000
cpu_shares: no shares
memory_limit_in_bytes: unlimited
memory_and_swap_limit_in_bytes: unlimited
memory_soft_limit_in_bytes: unlimited
memory_usage_in_bytes: 1499803873280
memory_max_usage_in_bytes: 2129504075776
maximum number of tasks: unlimited
current number of tasks: 1052
Steal ticks since vm start: 0
Steal ticks percentage since vm start: 0.000
CPU: total 160 (initial active 160) (20 cores per cpu, 2 threads per core) family 6 model 85 stepping 7 microcode 0x5003303, cx8, cmov, fxsr, ht, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, tscinvbit, avx, avx2, aes, erms, clmul, bmi1, bmi2, rtm, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb
CPU Model and flags from /proc/cpuinfo:
model name : Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin ssbd mba rsb_ctxsw ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities
Online cpus: 0-159
Offline cpus: 160-383
BIOS frequency limitation: <Not Available>
Frequency switch latency (ns): 4294967295
Available cpu frequencies: <Not Available>
Current governor: performance
Core performance/turbo boost: <Not Available>
Memory: 4k page, physical 2112944968k(601768876k free), swap 0k(0k free)
Page Sizes: 4k
vm_info: OpenJDK 64-Bit Server VM (18.0.1+10) for linux-amd64 JRE (18.0.1+10), built on May 12 2022 23:00:03 by "mockbuild" with gcc 8.3.1 20190311 (Red Hat 8.3.1-3)
END.
-
I see that you are using a JDK version above version 17 for 4.4.0.0 and above version 1.8 for 4.3.0.0. One recommendation we have (although you seem to have problems at a certain interval for only certain samples) is to use temurin JDK 17 from eclipse which is the officially supported version for 4.4.0.0. PairHMM Segfaults were noticed by our team and other users as well and most common solution is to use the temurin JDK (former adoptium) versions from https://adoptium.net/temurin website.
If this does not help we may ask you to send a slice of your bam files especially the problematic region so that we may test and see if we can reproduce the issue in our hands.
We hope this helps.
-
As a current workaround for this problem, is it possible for you to try to call that region using the following parameter with HaplotypeCaller
--pair-hmm-implementation LOGLESS_CACHING
This will disable OpenMP AVX accelerated pairHMM implementation and fall back to Java implementation which is slower but at least it may give us some idea.
Regards.
-
Hello Gökalp Çelik
Adding the LOGLESS_CACHING parameter totally worked - it was able to march through the problematic region with no issues.
I checked the output gvcf and it looked normal (the 100kb before the problem region had 2208 variant lines in the gvcf, compared to 2709 in the 100kb problem region).
Thanks for the workaround! Do you have any sense of what the problem might be?
-
We are glad that the workaround solved your problem. It is possible that there is an edge case in the native AVX accelerated library causing a segfault. We will relay this issue to GKL developers and let them check.
Thank you for reporting back.
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