A fatal error was detected by the Java Runtime Environment when running HaplotypeCaller
Hello- I have been trying to get Haplotype Caller to work for a couple of weeks now and can't seem to figure out the issue. I spoke to my institution's computing resources team and they suggested I submit a ticket here. Previous steps include: MarkIlluminaAdapters, BWA-mem, MergeBamAlignment, MarkDuplicates, BaseRecalibrator, ApplyBQSR, and merging bam files using samtools to create the input file for HaplotypeCaller. I would appreciate any help in determining how to work through the error I am getting.
Note: I have tried the command below with and without the following flags: -Xmx10G, --pair-hmm-implementation LOGLESS_CACHING
REQUIRED for all errors and issues:
a) GATK version used: 4.4.0.0
b) Exact command used:
#path to reference genome
ref=/path/to/ref_genome
java -Xmx10G -jar ${GATK} HaplotypeCaller \
-R $ref \
-I F_2650_final.bam \
--pair-hmm-implementation LOGLESS_CACHING \
-O F_2650_output.vcf.gz \
-bamout F_2650_aligned_output.bam
c) Entire program log:
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f2992158c7b, pid=20119, tid=20262
#
# JRE version: OpenJDK Runtime Environment (17.0.2+8) (build 17.0.2+8-86)
# Java VM: OpenJDK 64-Bit Server VM (17.0.2+8-86, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, serial gc, linux-amd64)
# Problematic frame:
# V [libjvm.so+0xb37c7b] markWord::displaced_mark_helper() const+0xb
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %e" (or dumping to /scratch/kmillan/WES/data/core.20119)
#
# If you would like to submit a bug report, please visit:
# https://bugreport.java.com/bugreport/crash.jsp
#
--------------- S U M M A R Y ------------
Command Line: -Xmx10G /apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R /scratch/kmillan/WES/ref_genome/Homo_sapiens.GRCh38.dna.toplevel.fa -I Merged_S14.bam --pair-hmm-implementation LOGLESS_CACHING -O Merged_output_S14.vcf.gz -bamout Merged_aligned_output_S14.bam
Host: Intel(R) Xeon(R) Gold 6326 CPU @ 2.90GHz, 32 cores, 125G, Red Hat Enterprise Linux release 8.3 (Ootpa)
Time: Wed Nov 29 16:01:40 2023 CST elapsed time: 182783.434444 seconds (2d 2h 46m 23s)
--------------- T H R E A D ---------------
Current thread (0x00007f298c059ee0): VMThread "VM Thread" [stack: 0x00007f2990136000,0x00007f2990236000] [id=20262]
Stack: [0x00007f2990136000,0x00007f2990236000], sp=0x00007f2990233f08, free space=1015k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0xb37c7b] markWord::displaced_mark_helper() const+0xb
V [libjvm.so+0x5e26d0] void OopOopIterateDispatch<DefNewScanClosure>::Table::oop_oop_iterate<InstanceKlass, narrowOop>(DefNewScanClosure*, oopDesc*, Klass*)+0xf0
V [libjvm.so+0x5e4b37] void ContiguousSpace::oop_since_save_marks_iterate<DefNewScanClosure>(DefNewScanClosure*)+0x97
V [libjvm.so+0x5dfe9e] DefNewGeneration::FastEvacuateFollowersClosure::do_void()+0xae
V [libjvm.so+0x5e0380] DefNewGeneration::collect(bool, bool, unsigned long, bool)+0x440
V [libjvm.so+0x75ab2d] GenCollectedHeap::collect_generation(Generation*, bool, unsigned long, bool, bool, bool, bool)+0x2cd
V [libjvm.so+0x75b666] GenCollectedHeap::do_collection(bool, bool, unsigned long, bool, GenCollectedHeap::GenerationType)+0x576
V [libjvm.so+0x75be3f] GenCollectedHeap::satisfy_failed_allocation(unsigned long, bool)+0xaf
V [libjvm.so+0x751265] VM_GenCollectForAllocation::doit()+0x45
V [libjvm.so+0xe13b6a] VM_Operation::evaluate()+0xea
V [libjvm.so+0xe15488] VMThread::evaluate_operation(VM_Operation*)+0xb8
V [libjvm.so+0xe15964] VMThread::inner_execute(VM_Operation*)+0x1d4
V [libjvm.so+0xe15c4f] VMThread::run()+0xbf
V [libjvm.so+0xd94e6e] Thread::call_run()+0xde
V [libjvm.so+0xbeae11] thread_native_entry(Thread*)+0xe1
siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0033003736333334
Register to memory mapping:
RAX=0x0033003736333334 is an unknown value
RBX=0x00000005a6779968 is an oop: [B
{0x00000005a6779968} - klass: {type array byte}
- length: 16
RCX=0x00000000c0100800 is an unknown value
RDX=0x00000000fffffff8 is an unknown value
RSP=0x00007f2990233f08 points into unknown readable memory: 0x00007f2991c008c5 | c5 08 c0 91 29 7f 00 00
RBP=0x00007f2990233f50 points into unknown readable memory: 0x00007f2990233fa0 | a0 3f 23 90 29 7f 00 00
RSI=0x00000005a6779968 is an oop: [B
{0x00000005a6779968} - klass: {type array byte}
- length: 16
RDI=0x00007f2990233f18 points into unknown readable memory: 0x0033003736333336 | 36 33 33 36 37 00 33 00
R8 =0xfffffffffffffff0 is an unknown value
R9 =0x00000005a18b00c0 is pointing into object: [B
{0x00000005a18b00b0} - klass: {type array byte}
- length: 14025
R10=0x00007f298c05a8c0 points into unknown readable memory: 0x0000000000000003 | 03 00 00 00 00 00 00 00
R11=0x00000005a18b3790 is an oop: [B
{0x00000005a18b3790} - klass: {type array byte}
- length: 32768
R12=0x0000000801203db8 is pointing into metadata
R13=0x0000000000000004 is an unknown value
R14=0x00007f298c03b920 points into unknown readable memory: 0x00007f29927f57f0 | f0 57 7f 92 29 7f 00 00
R15=0x0000000000000004 is an unknown value
Registers:
RAX=0x0033003736333334, RBX=0x00000005a6779968, RCX=0x00000000c0100800, RDX=0x00000000fffffff8
RSP=0x00007f2990233f08, RBP=0x00007f2990233f50, RSI=0x00000005a6779968, RDI=0x00007f2990233f18
R8 =0xfffffffffffffff0, R9 =0x00000005a18b00c0, R10=0x00007f298c05a8c0, R11=0x00000005a18b3790
R12=0x0000000801203db8, R13=0x0000000000000004, R14=0x00007f298c03b920, R15=0x0000000000000004
RIP=0x00007f2992158c7b, EFLAGS=0x0000000000010202, CSGSFS=0x002b000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00007f2990233f08)
0x00007f2990233f08: 00007f2991c008c5 0000000655550000
0x00007f2990233f18: 0033003736333336 0000000000000005
0x00007f2990233f28: 00007f2990234140 0000000801203db8
0x00007f2990233f38: 00000005a187ee14 00007f29928052f0
Instructions: (pc=0x00007f2992158c7b)
0x00007f2992158b7b: 61 b4 6f 00 e9 9f fd ff ff 48 89 f0 48 c1 e8 08
0x00007f2992158b8b: a9 ff ff ff 7f 0f 84 21 fd ff ff e9 14 fd ff ff
0x00007f2992158b9b: 48 8d 3d 1e b4 6f 00 e8 49 7a 8e ff b8 01 00 00
0x00007f2992158bab: 00 31 d2 e9 3a fc ff ff 48 8b 53 08 e9 e7 fd ff
0x00007f2992158bbb: ff 48 8b 43 08 e9 24 fe ff ff 48 89 f0 48 c1 e8
0x00007f2992158bcb: 08 a9 ff ff ff 7f 0f 84 92 fe ff ff e9 85 fe ff
0x00007f2992158bdb: ff 48 8d 3d dd b3 6f 00 e8 08 7a 8e ff b8 01 00
0x00007f2992158beb: 00 00 31 d2 e9 95 fe ff ff 48 8d 3d c5 b3 6f 00
0x00007f2992158bfb: e8 f0 79 8e ff b8 01 00 00 00 31 d2 e9 cb fc ff
0x00007f2992158c0b: ff 48 8b 43 08 e9 32 fe ff ff 48 8b 43 08 e9 77
0x00007f2992158c1b: fc ff ff 48 8d 3d 9b b3 6f 00 e8 c6 79 8e ff b8
0x00007f2992158c2b: 01 00 00 00 31 d2 e9 37 ff ff ff 48 89 f0 48 c1
0x00007f2992158c3b: e8 08 a9 ff ff ff 7f 0f 84 05 ff ff ff e9 f8 fe
0x00007f2992158c4b: ff ff 48 8b 43 08 e9 d5 fe ff ff 66 2e 0f 1f 84
0x00007f2992158c5b: 00 00 00 00 00 66 2e 0f 1f 84 00 00 00 00 00 00
0x00007f2992158c6b: 00 00 00 00 00 48 8b 07 a8 02 74 09 48 83 f0 02
0x00007f2992158c7b: 48 8b 00 c3 90 a8 03 75 0c 48 8b 00 c3 0f 1f 84
0x00007f2992158c8b: 00 00 00 00 00 55 48 8d 0d a0 85 38 00 ba 2b 00
0x00007f2992158c9b: 00 00 48 8d 35 d4 5c 3d 00 48 89 e5 53 48 89 fb
0x00007f2992158cab: 48 83 ec 08 48 8d 05 52 c6 6a 00 48 8b 00 c6 00
0x00007f2992158cbb: 58 4c 8b 07 31 c0 bf 00 00 00 e0 e8 f5 f5 a9 ff
0x00007f2992158ccb: e8 60 d9 0a 00 48 8b 03 48 8b 5d f8 c9 c3 90 66
0x00007f2992158cdb: 0f 1f 44 00 00 48 8b 07 a8 02 75 49 a8 03 75 05
0x00007f2992158ceb: 48 89 30 c3 90 48 8d 05 11 c6 6a 00 55 48 8d 0d
0x00007f2992158cfb: 39 85 38 00 ba 3d 00 00 00 48 8d 35 6d 5c 3d 00
0x00007f2992158d0b: 48 8b 00 48 89 e5 c6 00 58 4c 8b 07 31 c0 bf 00
0x00007f2992158d1b: 00 00 e0 e8 9d f5 a9 ff 5d e9 07 d9 0a 00 0f 1f
0x00007f2992158d2b: 80 00 00 00 00 48 83 f0 02 48 89 30 c3 0f 1f 84
0x00007f2992158d3b: 00 00 00 00 00 55 48 89 e5 41 55 49 89 f5 48 8d
0x00007f2992158d4b: 35 fc 84 38 00 41 54 41 89 d4 53 48 83 ec 08 48
0x00007f2992158d5b: 8b 17 48 89 d0 83 e0 03 48 83 f8 03 74 15 48 89
0x00007f2992158d6b: fb f6 c2 02 75 27 48 83 f8 01 74 61 48 8d 35 f4
Stack slot to memory mapping:
stack at sp + 0 slots: 0x00007f2991c008c5: <offset 0x00000000005df8c5> in /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so at 0x00007f2991621000
stack at sp + 1 slots: 0x0000000655550000 is an oop: [Ljava.lang.Object;
{0x0000000655550000} - klass: 'java/lang/Object'[]
- length: 3
stack at sp + 2 slots: 0x0033003736333336 is an unknown value
stack at sp + 3 slots: 0x0000000000000005 is an unknown value
stack at sp + 4 slots: 0x00007f2990234140 points into unknown readable memory: 0x00007f2992754920 | 20 49 75 92 29 7f 00 00
stack at sp + 5 slots: 0x0000000801203db8 is pointing into metadata
stack at sp + 6 slots: 0x00000005a187ee14 is pointing into object: org.xerial.snappy.SnappyInputStream
{0x00000005a187edf0} - klass: 'org/xerial/snappy/SnappyInputStream'
- ---- fields (total size 5 words):
- private 'uncompressedCursor' 'I' @12 27997 (6d5d)
- private 'uncompressedLimit' 'I' @16 32768 (8000)
- private 'finishedReading' 'Z' @20 false
- protected final 'in' 'Ljava/io/InputStream;' @24 a 'java/io/BufferedInputStream'{0x00000005a18b0088} (b4316011)
- private 'compressed' '[B' @28 [B{0x00000005a18b00b0} (b4316016)
- private 'uncompressed' '[B' @32 [B{0x00000005a18b3790} (b43166f2)
- private 'header' '[B' @36 [B{0x00000005a6779968} (b4cef32d)
stack at sp + 7 slots: 0x00007f29928052f0: <offset 0x00000000011e42f0> in /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so at 0x00007f2991621000
VM_Operation (0x00007f299348af00): GenCollectForAllocation, mode: safepoint, requested by thread 0x00007f298c023de0
--------------- P R O C E S S ---------------
Threads class SMR info:
_java_thread_list=0x00007f293800a320, length=11, elements={
0x00007f298c023de0, 0x00007f298c05e6d0, 0x00007f298c05fae0, 0x00007f298c069750,
0x00007f298c06aad0, 0x00007f298c06beb0, 0x00007f298c06d830, 0x00007f298c06ed30,
0x00007f298c070170, 0x00007f298c0ac530, 0x00007f298c0af390
}
Java Threads: ( => current thread )
0x00007f298c023de0 JavaThread "main" [_thread_blocked, id=20120, stack(0x00007f299338c000,0x00007f299348d000)]
0x00007f298c05e6d0 JavaThread "Reference Handler" daemon [_thread_blocked, id=20266, stack(0x00007f2990033000,0x00007f2990134000)]
0x00007f298c05fae0 JavaThread "Finalizer" daemon [_thread_blocked, id=20267, stack(0x00007f29734bd000,0x00007f29735be000)]
0x00007f298c069750 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=20276, stack(0x00007f2972aff000,0x00007f2972c00000)]
0x00007f298c06aad0 JavaThread "Service Thread" daemon [_thread_blocked, id=20278, stack(0x00007f29729fe000,0x00007f2972aff000)]
0x00007f298c06beb0 JavaThread "Monitor Deflation Thread" daemon [_thread_blocked, id=20279, stack(0x00007f29728fd000,0x00007f29729fe000)]
0x00007f298c06d830 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=20280, stack(0x00007f29727fc000,0x00007f29728fd000)]
0x00007f298c06ed30 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=20281, stack(0x00007f29726fb000,0x00007f29727fc000)]
0x00007f298c070170 JavaThread "Sweeper thread" daemon [_thread_blocked, id=20283, stack(0x00007f29725fa000,0x00007f29726fb000)]
0x00007f298c0ac530 JavaThread "Notification Thread" daemon [_thread_blocked, id=20285, stack(0x00007f29724f9000,0x00007f29725fa000)]
0x00007f298c0af390 JavaThread "Common-Cleaner" daemon [_thread_blocked, id=20289, stack(0x00007f29722f6000,0x00007f29723f7000)]
Other Threads:
=>0x00007f298c059ee0 VMThread "VM Thread" [stack: 0x00007f2990136000,0x00007f2990236000] [id=20262]
0x00007f298c0ade50 WatcherThread [stack: 0x00007f29723f9000,0x00007f29724f9000] [id=20288]
Threads with active compile tasks:
VM state: at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[0x00007f298c0209a0] Threads_lock - owner thread: 0x00007f298c059ee0
[0x00007f298c021150] Heap_lock - owner thread: 0x00007f298c023de0
Heap address: 0x0000000580000000, size: 10240 MB, Compressed Oops mode: Zero based, Oop shift amount: 3
CDS archive(s) mapped at: [0x0000000800000000-0x0000000800bde000-0x0000000800bde000), size 12443648, 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:
CPUs: 32 total, 1 available
Memory: 125G
Large Page Support: Disabled
NUMA Support: Disabled
Compressed Oops: Enabled (Zero based)
Heap Min Capacity: 8M
Heap Initial Capacity: 2010M
Heap Max Capacity: 10G
Pre-touch: Disabled
Heap:
def new generation total 617536K, used 565061K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 23% used [0x00000005a5b10000, 0x00000005a6ad1448, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a18bb7a0, 0x00000005a5b10000)
tenured generation total 1372160K, used 184382K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 13% used [0x0000000655550000, 0x000000066095fa58, 0x000000066095fc00, 0x00000006a9150000)
Metaspace used 47860K, committed 48192K, reserved 1097728K
class space used 6118K, committed 6272K, reserved 1048576K
Card table byte_map: [0x00007f2974314000,0x00007f2975715000] _byte_map_base: 0x00007f2971714000
Polling page: 0x00007f29934af000
Metaspace:
Usage:
Non-class: 40.76 MB used.
Class: 5.98 MB used.
Both: 46.74 MB used.
Virtual space:
Non-class space: 48.00 MB reserved, 40.94 MB ( 85%) committed, 6 nodes.
Class space: 1.00 GB reserved, 6.12 MB ( <1%) committed, 1 nodes.
Both: 1.05 GB reserved, 47.06 MB ( 4%) committed.
Chunk freelists:
Non-Class: 2.42 MB
Class: 1.85 MB
Both: 4.27 MB
MaxMetaspaceSize: unlimited
CompressedClassSpaceSize: 1.00 GB
Initial GC threshold: 21.00 MB
Current GC threshold: 78.38 MB
CDS: on
MetaspaceReclaimPolicy: balanced
- commit_granule_bytes: 65536.
- commit_granule_words: 8192.
- virtual_space_node_default_size: 1048576.
- enlarge_chunks_in_place: 1.
- new_chunks_are_fully_committed: 0.
- uncommit_free_chunks: 1.
- use_allocation_guard: 0.
- handle_deallocations: 1.
Internal statistics:
num_allocs_failed_limit: 6.
num_arena_births: 522.
num_arena_deaths: 134.
num_vsnodes_births: 7.
num_vsnodes_deaths: 0.
num_space_committed: 752.
num_space_uncommitted: 0.
num_chunks_returned_to_freelist: 157.
num_chunks_taken_from_freelist: 2044.
num_chunk_merges: 56.
num_chunk_splits: 1549.
num_chunks_enlarged: 1275.
num_purges: 2.
num_inconsistent_stats: 0.
CodeHeap 'non-profiled nmethods': size=120036Kb used=11694Kb max_used=11694Kb free=108341Kb
bounds [0x00007f297d1dc000, 0x00007f297dd6c000, 0x00007f2984715000]
CodeHeap 'profiled nmethods': size=120032Kb used=8527Kb max_used=11882Kb free=111504Kb
bounds [0x00007f2975ca4000, 0x00007f2976844000, 0x00007f297d1dc000]
CodeHeap 'non-nmethods': size=5692Kb used=1327Kb max_used=1390Kb free=4364Kb
bounds [0x00007f2975715000, 0x00007f2975985000, 0x00007f2975ca4000]
total_blobs=7129 nmethods=6473 adapters=571
compilation: enabled
stopped_count=0, restarted_count=0
full_count=0
Compilation events (20 events):
Event: 182781.075 Thread 0x00007f298c06d830 10882 4 org.xerial.snappy.pure.PureJavaSnappy::rawUncompress (47 bytes)
Event: 182781.076 Thread 0x00007f298c06d830 nmethod 10882 0x00007f297d478f90 code [0x00007f297d479120, 0x00007f297d479448]
Event: 182781.076 Thread 0x00007f298c06d830 10883 4 org.xerial.snappy.pure.SnappyRawDecompressor::decompress (140 bytes)
Event: 182781.078 Thread 0x00007f298c06d830 nmethod 10883 0x00007f297d478790 code [0x00007f297d478920, 0x00007f297d478c68]
Event: 182781.756 Thread 0x00007f298c06ed30 10884 3 htsjdk.samtools.util.PeekIterator::peek (25 bytes)
Event: 182781.756 Thread 0x00007f298c06ed30 nmethod 10884 0x00007f2976553b90 code [0x00007f2976553d40, 0x00007f2976553f80]
Event: 182781.758 Thread 0x00007f298c06d830 10885 4 htsjdk.samtools.util.PeekIterator::peek (25 bytes)
Event: 182781.779 Thread 0x00007f298c06ed30 10886 ! 3 htsjdk.samtools.BAMRecordCodec::decode (223 bytes)
Event: 182781.780 Thread 0x00007f298c06ed30 nmethod 10886 0x00007f29763f2590 code [0x00007f29763f2b40, 0x00007f29763f5670]
Event: 182781.782 Thread 0x00007f298c06ed30 10887 % ! 3 htsjdk.samtools.SAMFileWriterImpl::close @ 22 (110 bytes)
Event: 182781.782 Thread 0x00007f298c06ed30 nmethod 10887% 0x00007f2975e4f190 code [0x00007f2975e4f480, 0x00007f2975e50770]
Event: 182781.934 Thread 0x00007f298c06d830 nmethod 10885 0x00007f297dd49090 code [0x00007f297dd49820, 0x00007f297dd50bc0]
Event: 182781.935 Thread 0x00007f298c06d830 10890 ! 4 htsjdk.samtools.BAMRecordCodec::decode (223 bytes)
Event: 182782.159 Thread 0x00007f298c06d830 nmethod 10890 0x00007f297dd56290 code [0x00007f297dd56a20, 0x00007f297dd5cce0]
Event: 182782.159 Thread 0x00007f298c06d830 10889 4 htsjdk.samtools.BAMRecordCodec::decode (5 bytes)
Event: 182782.160 Thread 0x00007f298c06d830 nmethod 10889 0x00007f297d478490 code [0x00007f297d478620, 0x00007f297d4786c8]
Event: 182782.160 Thread 0x00007f298c06d830 10888 4 htsjdk.samtools.util.SortingCollection$FileRecordIterator::next (26 bytes)
Event: 182782.160 Thread 0x00007f298c06d830 nmethod 10888 0x00007f297d478090 code [0x00007f297d478220, 0x00007f297d478348]
Event: 182782.175 Thread 0x00007f298c06d830 10891 % ! 4 htsjdk.samtools.SAMFileWriterImpl::close @ 22 (110 bytes)
Event: 182782.182 Thread 0x00007f298c06d830 nmethod 10891% 0x00007f297d89f310 code [0x00007f297d89f520, 0x00007f297d89fbd0]
GC Heap History (20 events):
Event: 182731.671 GC heap after
{Heap after GC invocations=79039 (full 94):
def new generation total 617536K, used 11436K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 16% used [0x00000005a5b10000, 0x00000005a663b238, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182732.091 GC heap before
{Heap before GC invocations=79039 (full 94):
def new generation total 617536K, used 560364K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 16% used [0x00000005a5b10000, 0x00000005a663b238, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182732.105 GC heap after
{Heap after GC invocations=79040 (full 94):
def new generation total 617536K, used 17884K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 26% used [0x00000005a1810000, 0x00000005a29871e0, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182751.229 GC heap before
{Heap before GC invocations=79040 (full 94):
def new generation total 617536K, used 566812K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 26% used [0x00000005a1810000, 0x00000005a29871e0, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182751.241 GC heap after
{Heap after GC invocations=79041 (full 94):
def new generation total 617536K, used 19422K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 28% used [0x00000005a5b10000, 0x00000005a6e07b38, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182756.936 GC heap before
{Heap before GC invocations=79041 (full 94):
def new generation total 617536K, used 568350K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 28% used [0x00000005a5b10000, 0x00000005a6e07b38, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182756.947 GC heap after
{Heap after GC invocations=79042 (full 94):
def new generation total 617536K, used 18620K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 27% used [0x00000005a1810000, 0x00000005a2a3f010, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182761.436 GC heap before
{Heap before GC invocations=79042 (full 94):
def new generation total 617536K, used 567548K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 27% used [0x00000005a1810000, 0x00000005a2a3f010, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182761.446 GC heap after
{Heap after GC invocations=79043 (full 94):
def new generation total 617536K, used 17440K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 25% used [0x00000005a5b10000, 0x00000005a6c18080, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47670K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182762.472 GC heap before
{Heap before GC invocations=79043 (full 94):
def new generation total 617536K, used 566368K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 25% used [0x00000005a5b10000, 0x00000005a6c18080, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182762.482 GC heap after
{Heap after GC invocations=79044 (full 94):
def new generation total 617536K, used 17171K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 25% used [0x00000005a1810000, 0x00000005a28d4c30, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182762.921 GC heap before
{Heap before GC invocations=79044 (full 94):
def new generation total 617536K, used 566099K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 25% used [0x00000005a1810000, 0x00000005a28d4c30, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182762.933 GC heap after
{Heap after GC invocations=79045 (full 94):
def new generation total 617536K, used 19606K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 28% used [0x00000005a5b10000, 0x00000005a6e358a0, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182768.514 GC heap before
{Heap before GC invocations=79045 (full 94):
def new generation total 617536K, used 568534K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 28% used [0x00000005a5b10000, 0x00000005a6e358a0, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 1233413K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a09d17d0, 0x00000006a09d1800, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182768.527 GC heap after
{Heap after GC invocations=79046 (full 94):
def new generation total 617536K, used 21486K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 31% used [0x00000005a1810000, 0x00000005a2d0b960, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1234055K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a0a71cf0, 0x00000006a0a71e00, 0x00000006a9150000)
Metaspace used 47672K, committed 48064K, reserved 1097728K
class space used 6097K, committed 6272K, reserved 1048576K
}
Event: 182776.833 GC heap before
{Heap before GC invocations=79046 (full 94):
def new generation total 617536K, used 395141K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 68% used [0x0000000580000000, 0x0000000596ce5b20, 0x00000005a1810000)
from space 68608K, 31% used [0x00000005a1810000, 0x00000005a2d0b960, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 1234055K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 89% used [0x0000000655550000, 0x00000006a0a71cf0, 0x00000006a0a71e00, 0x00000006a9150000)
Metaspace used 47771K, committed 48128K, reserved 1097728K
class space used 6112K, committed 6272K, reserved 1048576K
}
Event: 182777.146 GC heap after
{Heap after GC invocations=79047 (full 95):
def new generation total 617536K, used 0K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 184382K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 13% used [0x0000000655550000, 0x000000066095fa58, 0x000000066095fc00, 0x00000006a9150000)
Metaspace used 47771K, committed 48128K, reserved 1097728K
class space used 6112K, committed 6272K, reserved 1048576K
}
Event: 182780.521 GC heap before
{Heap before GC invocations=79047 (full 95):
def new generation total 617536K, used 548928K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
to space 68608K, 0% used [0x00000005a5b10000, 0x00000005a5b10000, 0x00000005a9e10000)
tenured generation total 1372160K, used 184382K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 13% used [0x0000000655550000, 0x000000066095fa58, 0x000000066095fc00, 0x00000006a9150000)
Metaspace used 47860K, committed 48192K, reserved 1097728K
class space used 6118K, committed 6272K, reserved 1048576K
}
Event: 182780.524 GC heap after
{Heap after GC invocations=79048 (full 95):
def new generation total 617536K, used 16133K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 0% used [0x0000000580000000, 0x0000000580000000, 0x00000005a1810000)
from space 68608K, 23% used [0x00000005a5b10000, 0x00000005a6ad1448, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 184382K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 13% used [0x0000000655550000, 0x000000066095fa58, 0x000000066095fc00, 0x00000006a9150000)
Metaspace used 47860K, committed 48192K, reserved 1097728K
class space used 6118K, committed 6272K, reserved 1048576K
}
Event: 182783.409 GC heap before
{Heap before GC invocations=79048 (full 95):
def new generation total 617536K, used 565061K [0x0000000580000000, 0x00000005a9e10000, 0x0000000655550000)
eden space 548928K, 100% used [0x0000000580000000, 0x00000005a1810000, 0x00000005a1810000)
from space 68608K, 23% used [0x00000005a5b10000, 0x00000005a6ad1448, 0x00000005a9e10000)
to space 68608K, 0% used [0x00000005a1810000, 0x00000005a1810000, 0x00000005a5b10000)
tenured generation total 1372160K, used 184382K [0x0000000655550000, 0x00000006a9150000, 0x0000000800000000)
the space 1372160K, 13% used [0x0000000655550000, 0x000000066095fa58, 0x000000066095fc00, 0x00000006a9150000)
Metaspace used 47860K, committed 48192K, reserved 1097728K
class space used 6118K, committed 6272K, reserved 1048576K
}
Deoptimization events (20 events):
Event: 182779.831 Thread 0x00007f298c023de0 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f297d485c64 relative=0x0000000000000364
Event: 182779.831 Thread 0x00007f298c023de0 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f297d485c64 method=htsjdk.samtools.util.SortingCollection$FileRecordIterator.hasNext()Z @ 4 c2
Event: 182779.831 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f297d485c64 sp=0x00007f299348b290
Event: 182779.831 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576a599 sp=0x00007f299348b120 mode 2
Event: 182779.831 Thread 0x00007f298c023de0 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f297d4899a4 relative=0x00000000000001e4
Event: 182779.831 Thread 0x00007f298c023de0 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f297d4899a4 method=java.util.TreeMap.deleteEntry(Ljava/util/TreeMap$Entry;)V @ 77 c2
Event: 182779.831 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f297d4899a4 sp=0x00007f299348b210
Event: 182779.831 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576a599 sp=0x00007f299348b088 mode 2
Event: 182780.025 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f29765b31ac sp=0x00007f299348b220
Event: 182780.025 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576b0cf sp=0x00007f299348a748 mode 0
Event: 182781.750 Thread 0x00007f298c023de0 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f297d9b12dc relative=0x00000000000051bc
Event: 182781.750 Thread 0x00007f298c023de0 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f297d9b12dc method=org.xerial.snappy.SnappyInputStream.read([BII)I @ 24 c2
Event: 182781.750 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f297d9b12dc sp=0x00007f299348b0e0
Event: 182781.750 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576a599 sp=0x00007f299348ad20 mode 2
Event: 182781.756 Thread 0x00007f298c023de0 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007f297d479de4 relative=0x0000000000000444
Event: 182781.756 Thread 0x00007f298c023de0 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f297d479de4 method=java.util.TreeMap.deleteEntry(Ljava/util/TreeMap$Entry;)V @ 184 c2
Event: 182781.756 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f297d479de4 sp=0x00007f299348b290
Event: 182781.756 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576a599 sp=0x00007f299348b090 mode 2
Event: 182782.182 Thread 0x00007f298c023de0 DEOPT PACKING pc=0x00007f2975e5042c sp=0x00007f299348b220
Event: 182782.182 Thread 0x00007f298c023de0 DEOPT UNPACKING pc=0x00007f297576b0cf sp=0x00007f299348a748 mode 0
Classes unloaded (20 events):
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1e400 'java/lang/invoke/LambdaForm$MH+0x0000000800d1e400'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1dc00 'java/lang/invoke/LambdaForm$MH+0x0000000800d1dc00'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1d000 'java/lang/invoke/LambdaForm$MH+0x0000000800d1d000'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1cc00 'java/lang/invoke/LambdaForm$MH+0x0000000800d1cc00'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1c800 'java/lang/invoke/LambdaForm$MH+0x0000000800d1c800'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d1c400 'java/lang/invoke/LambdaForm$MH+0x0000000800d1c400'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d10400 'java/lang/invoke/LambdaForm$MH+0x0000000800d10400'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d10000 'java/lang/invoke/LambdaForm$MH+0x0000000800d10000'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0fc00 'java/lang/invoke/LambdaForm$MH+0x0000000800d0fc00'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0f800 'java/lang/invoke/LambdaForm$MH+0x0000000800d0f800'
Event: 10029.347 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0f400 'java/lang/invoke/LambdaForm$MH+0x0000000800d0f400'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0f000 'java/lang/invoke/LambdaForm$MH+0x0000000800d0f000'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0e800 'java/lang/invoke/LambdaForm$MH+0x0000000800d0e800'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0e000 'java/lang/invoke/LambdaForm$MH+0x0000000800d0e000'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0dc00 'java/lang/invoke/LambdaForm$MH+0x0000000800d0dc00'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0d800 'java/lang/invoke/LambdaForm$MH+0x0000000800d0d800'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0d000 'java/lang/invoke/LambdaForm$MH+0x0000000800d0d000'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0cc00 'java/lang/invoke/LambdaForm$MH+0x0000000800d0cc00'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0c800 'java/lang/invoke/LambdaForm$MH+0x0000000800d0c800'
Event: 10029.348 Thread 0x00007f298c059ee0 Unloading class 0x0000000800d0c000 'java/lang/invoke/LambdaForm$MH+0x0000000800d0c000'
Classes redefined (0 events):
No events
Internal exceptions (20 events):
Event: 17.795 Thread 0x00007f298c023de0 Exception <a 'java/lang/NoSuchMethodError'{0x000000058c318848}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, double)'> (0x000000058c318848)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 17.797 Thread 0x00007f298c023de0 Exception <a 'java/lang/NoSuchMethodError'{0x000000058c3422a0}: 'double java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object)'> (0x000000058c3422a0)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 25.367 Thread 0x00007f298c023de0 Exception <a 'java/lang/NoSuchMethodError'{0x0000000582e85e60}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(java.lang.Object, java.lang.Object, java.lang.Object)'> (0x0000000582e85e60)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 87.997 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d5c0dd6 to 0x00007f297d5c0f7c
Event: 387.539 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d762c8c to 0x00007f297d764124
Event: 781.171 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d939d93 to 0x00007f297d939ff4
Event: 1867.210 Thread 0x00007f298d1b9ef0 Implicit null exception at 0x00007f297d6cfbfd to 0x00007f297d6cfd7c
Event: 1867.210 Thread 0x00007f298d1b9ef0 Implicit null exception at 0x00007f297d6cf680 to 0x00007f297d6cf7a0
Event: 1867.219 Thread 0x00007f298d1b9ef0 Exception <a 'java/lang/NoSuchMethodError'{0x00000005875f5610}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeStaticInit(java.lang.Object)'> (0x00000005875f5610)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 1867.303 Thread 0x00007f298d1b9ef0 Exception <a 'java/lang/UnsatisfiedLinkError'{0x000000058810f810}> (0x000000058810f810)
thrown [open/src/hotspot/share/prims/jvm.cpp, line 3381]
Event: 1867.303 Thread 0x00007f298d1b9ef0 Exception <a 'java/lang/UnsatisfiedLinkError'{0x000000058810f810}> (0x000000058810f810)
thrown [open/src/hotspot/share/prims/jni.cpp, line 516]
Event: 12338.424 Thread 0x00007f298c023de0 Exception <a 'java/lang/NoSuchMethodError'{0x000000058109ea68}: 'double java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object)'> (0x000000058109ea68)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 14804.313 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d89fff9 to 0x00007f297d8a3e40
Event: 18263.773 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d56d5b7 to 0x00007f297d56e22c
Event: 18263.811 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297dbf1fcc to 0x00007f297dbf3d68
Event: 18263.811 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d93eb0a to 0x00007f297d93ed8c
Event: 73282.921 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d28dcf6 to 0x00007f297d294364
Event: 112847.423 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d767d06 to 0x00007f297d767f14
Event: 182776.256 Thread 0x00007f298c023de0 Exception <a 'java/lang/NoSuchMethodError'{0x0000000595c49e10}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, int)'> (0x0000000595c49e10)
thrown [open/src/hotspot/share/interpreter/linkResolver.cpp, line 765]
Event: 182776.282 Thread 0x00007f298c023de0 Implicit null exception at 0x00007f297d791c9d to 0x00007f297d7920a4
VM Operations (20 events):
Event: 182762.933 Executing VM operation: GenCollectForAllocation done
Event: 182768.514 Executing VM operation: GenCollectForAllocation
Event: 182768.527 Executing VM operation: GenCollectForAllocation done
Event: 182776.527 Executing VM operation: Cleanup
Event: 182776.527 Executing VM operation: Cleanup done
Event: 182776.833 Executing VM operation: GenCollectFull
Event: 182777.146 Executing VM operation: GenCollectFull done
Event: 182778.147 Executing VM operation: Cleanup
Event: 182778.147 Executing VM operation: Cleanup done
Event: 182779.147 Executing VM operation: Cleanup
Event: 182779.147 Executing VM operation: Cleanup done
Event: 182780.147 Executing VM operation: Cleanup
Event: 182780.147 Executing VM operation: Cleanup done
Event: 182780.521 Executing VM operation: GenCollectForAllocation
Event: 182780.524 Executing VM operation: GenCollectForAllocation done
Event: 182781.750 Executing VM operation: HandshakeAllThreads
Event: 182781.750 Executing VM operation: HandshakeAllThreads done
Event: 182782.750 Executing VM operation: Cleanup
Event: 182782.750 Executing VM operation: Cleanup done
Event: 182783.409 Executing VM operation: GenCollectForAllocation
Events (20 events):
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29766c0d10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29766c3b90
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29766d0590
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29766f4510
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976706f10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f297673d490
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f297674ba10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f297675f410
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976764290
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29767e2f10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29767efc10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f29767fec10
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976814610
Event: 74639.099 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976827990
Event: 182776.704 Thread 0x00007f298d1b9ef0 Thread exited: 0x00007f298d1b9ef0
Event: 182781.754 Thread 0x00007f298c070170 flushing nmethod 0x00007f2975fe6890
Event: 182781.754 Thread 0x00007f298c070170 flushing nmethod 0x00007f29761f7e90
Event: 182781.755 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976553b90
Event: 182781.755 Thread 0x00007f298c070170 flushing nmethod 0x00007f29765bd290
Event: 182781.755 Thread 0x00007f298c070170 flushing nmethod 0x00007f2976716c90
Dynamic libraries:
580000000-5a9e10000 rw-p 00000000 00:00 0
5a9e10000-655550000 ---p 00000000 00:00 0
655550000-6a9150000 rw-p 00000000 00:00 0
6a9150000-800000000 ---p 00000000 00:00 0
800000000-800457000 rw-p 00001000 00:34 6888076647 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/classes.jsa
800457000-800bde000 r--p 00458000 00:34 6888076647 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/classes.jsa
800bde000-800c00000 ---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
800d40000-801170000 rw-p 00000000 00:00 0
801170000-801180000 ---p 00000000 00:00 0
801180000-801230000 rw-p 00000000 00:00 0
801230000-840c00000 ---p 00000000 00:00 0
558443203000-558443204000 r-xp 00000000 00:34 6887051125 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/bin/java
558443205000-558443206000 r--p 00001000 00:34 6887051125 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/bin/java
558443206000-558443207000 rw-p 00002000 00:34 6887051125 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/bin/java
558443e0f000-558443e30000 rw-p 00000000 00:00 0 [heap]
7f2938000000-7f2938064000 rw-p 00000000 00:00 0
7f2938064000-7f293c000000 ---p 00000000 00:00 0
7f293c000000-7f293c021000 rw-p 00000000 00:00 0
7f293c021000-7f2940000000 ---p 00000000 00:00 0
7f2941000000-7f29410a0000 rw-p 00000000 00:00 0
7f29410a0000-7f2941100000 ---p 00000000 00:00 0
7f2941100000-7f2941150000 rw-p 00000000 00:00 0
7f2941150000-7f2941800000 ---p 00000000 00:00 0
7f2941ae0000-7f2942800000 r--s 00000000 00:33 785041 /scratch/kmillan/WES/data/Merged_S14.bam.bai
7f2942800000-7f2942900000 rw-p 00000000 00:00 0
7f2942900000-7f2942a00000 rw-p 00000000 00:00 0
7f2942a00000-7f2942bc0000 rw-p 00000000 00:00 0
7f2942bc0000-7f2942c00000 rw-p 00000000 00:00 0
7f2942c00000-7f2942d00000 rw-p 00000000 00:00 0
7f2942d00000-7f2942e00000 rw-p 00000000 00:00 0
7f2942e00000-7f2943000000 rw-p 00000000 00:00 0
7f2943000000-7f2943800000 rw-p 00000000 00:00 0
7f2943800000-7f2944000000 rw-p 00000000 00:00 0
7f2944000000-7f2944021000 rw-p 00000000 00:00 0
7f2944021000-7f2948000000 ---p 00000000 00:00 0
7f2948000000-7f2948021000 rw-p 00000000 00:00 0
7f2948021000-7f294c000000 ---p 00000000 00:00 0
7f294c000000-7f294cacb000 rw-p 00000000 00:00 0
7f294cacb000-7f2950000000 ---p 00000000 00:00 0
7f2950000000-7f2950021000 rw-p 00000000 00:00 0
7f2950021000-7f2954000000 ---p 00000000 00:00 0
7f2954000000-7f2954021000 rw-p 00000000 00:00 0
7f2954021000-7f2958000000 ---p 00000000 00:00 0
7f2958000000-7f295af53000 rw-p 00000000 00:00 0
7f295af53000-7f295c000000 ---p 00000000 00:00 0
7f295c000000-7f295c021000 rw-p 00000000 00:00 0
7f295c021000-7f2960000000 ---p 00000000 00:00 0
7f2960000000-7f2960021000 rw-p 00000000 00:00 0
7f2960021000-7f2964000000 ---p 00000000 00:00 0
7f2964000000-7f2964021000 rw-p 00000000 00:00 0
7f2964021000-7f2968000000 ---p 00000000 00:00 0
7f2968000000-7f2968021000 rw-p 00000000 00:00 0
7f2968021000-7f296c000000 ---p 00000000 00:00 0
7f296c000000-7f296c4cd000 rw-p 00000000 00:00 0
7f296c4cd000-7f2970000000 ---p 00000000 00:00 0
7f29702ff000-7f2970303000 ---p 00000000 00:00 0
7f2970303000-7f29704c0000 rw-p 00000000 00:00 0
7f29704c0000-7f2970500000 rw-p 00000000 00:00 0
7f2970500000-7f2970700000 rw-p 00000000 00:00 0
7f2970700000-7f2970c00000 rw-p 00000000 00:00 0
7f2970caa000-7f2970d2d000 r-xp 00000000 fd:00 100669018 /usr/lib64/libpcre2-8.so.0.7.1
7f2970d2d000-7f2970f2c000 ---p 00083000 fd:00 100669018 /usr/lib64/libpcre2-8.so.0.7.1
7f2970f2c000-7f2970f2d000 r--p 00082000 fd:00 100669018 /usr/lib64/libpcre2-8.so.0.7.1
7f2970f2d000-7f2970f2e000 rw-p 00083000 fd:00 100669018 /usr/lib64/libpcre2-8.so.0.7.1
7f2970f2e000-7f2970f55000 r-xp 00000000 fd:00 100669024 /usr/lib64/libselinux.so.1
7f2970f55000-7f2971154000 ---p 00027000 fd:00 100669024 /usr/lib64/libselinux.so.1
7f2971154000-7f2971155000 r--p 00026000 fd:00 100669024 /usr/lib64/libselinux.so.1
7f2971155000-7f2971156000 rw-p 00027000 fd:00 100669024 /usr/lib64/libselinux.so.1
7f2971156000-7f2971158000 rw-p 00000000 00:00 0
7f2971158000-7f297115e000 r-xp 00000000 fd:00 100669408 /usr/lib64/libuuid.so.1.3.0
7f297115e000-7f297135e000 ---p 00006000 fd:00 100669408 /usr/lib64/libuuid.so.1.3.0
7f297135e000-7f297135f000 r--p 00006000 fd:00 100669408 /usr/lib64/libuuid.so.1.3.0
7f297135f000-7f2971360000 rw-p 00000000 00:00 0
7f2971360000-7f29713ac000 r-xp 00000000 fd:00 100718050 /usr/lib64/libblkid.so.1.1.0
7f29713ac000-7f29715ac000 ---p 0004c000 fd:00 100718050 /usr/lib64/libblkid.so.1.1.0
7f29715ac000-7f29715b1000 r--p 0004c000 fd:00 100718050 /usr/lib64/libblkid.so.1.1.0
7f29715b1000-7f29715b2000 rw-p 00051000 fd:00 100718050 /usr/lib64/libblkid.so.1.1.0
7f29715b2000-7f29715b3000 rw-p 00000000 00:00 0
7f29715b3000-7f29715ca000 r-xp 00000000 fd:00 100663430 /usr/lib64/libgcc_s-8-20191121.so.1
7f29715ca000-7f29717c9000 ---p 00017000 fd:00 100663430 /usr/lib64/libgcc_s-8-20191121.so.1
7f29717c9000-7f29717ca000 r--p 00016000 fd:00 100663430 /usr/lib64/libgcc_s-8-20191121.so.1
7f29717ca000-7f29717cb000 rw-p 00017000 fd:00 100663430 /usr/lib64/libgcc_s-8-20191121.so.1
7f29717cb000-7f2971820000 r-xp 00000000 fd:00 100717822 /usr/lib64/libmount.so.1.1.0
7f2971820000-7f2971a20000 ---p 00055000 fd:00 100717822 /usr/lib64/libmount.so.1.1.0
7f2971a20000-7f2971a23000 r--p 00055000 fd:00 100717822 /usr/lib64/libmount.so.1.1.0
7f2971a23000-7f2971a24000 rw-p 00058000 fd:00 100717822 /usr/lib64/libmount.so.1.1.0
7f2971a24000-7f2971a25000 rw-p 00000000 00:00 0
7f2971a25000-7f2971abf000 r-xp 00000000 fd:00 100717857 /usr/lib64/libnss_myhostname.so.2
7f2971abf000-7f2971cbf000 ---p 0009a000 fd:00 100717857 /usr/lib64/libnss_myhostname.so.2
7f2971cbf000-7f2971cc5000 r--p 0009a000 fd:00 100717857 /usr/lib64/libnss_myhostname.so.2
7f2971cc5000-7f2971cc6000 rw-p 000a0000 fd:00 100717857 /usr/lib64/libnss_myhostname.so.2
7f2971cc6000-7f2971cda000 r-xp 00000000 fd:00 100669145 /usr/lib64/libresolv-2.28.so
7f2971cda000-7f2971ed9000 ---p 00014000 fd:00 100669145 /usr/lib64/libresolv-2.28.so
7f2971ed9000-7f2971eda000 r--p 00013000 fd:00 100669145 /usr/lib64/libresolv-2.28.so
7f2971eda000-7f2971edb000 rw-p 00014000 fd:00 100669145 /usr/lib64/libresolv-2.28.so
7f2971edb000-7f2971edd000 rw-p 00000000 00:00 0
7f2971edd000-7f2971ee2000 r-xp 00000000 fd:00 100669139 /usr/lib64/libnss_dns-2.28.so
7f2971ee2000-7f29720e2000 ---p 00005000 fd:00 100669139 /usr/lib64/libnss_dns-2.28.so
7f29720e2000-7f29720e3000 r--p 00005000 fd:00 100669139 /usr/lib64/libnss_dns-2.28.so
7f29720e3000-7f29720e4000 rw-p 00006000 fd:00 100669139 /usr/lib64/libnss_dns-2.28.so
7f29720e4000-7f29720ef000 r-xp 00000000 fd:00 100669141 /usr/lib64/libnss_files-2.28.so
7f29720ef000-7f29722ee000 ---p 0000b000 fd:00 100669141 /usr/lib64/libnss_files-2.28.so
7f29722ee000-7f29722ef000 r--p 0000a000 fd:00 100669141 /usr/lib64/libnss_files-2.28.so
7f29722ef000-7f29722f0000 rw-p 0000b000 fd:00 100669141 /usr/lib64/libnss_files-2.28.so
7f29722f0000-7f29722f6000 rw-p 00000000 00:00 0
7f29722f6000-7f29722fa000 ---p 00000000 00:00 0
7f29722fa000-7f29723f7000 rw-p 00000000 00:00 0
7f29723f7000-7f29723f8000 ---p 00000000 00:00 0
7f29723f8000-7f29724f9000 rw-p 00000000 00:00 0
7f29724f9000-7f29724fd000 ---p 00000000 00:00 0
7f29724fd000-7f29725fa000 rw-p 00000000 00:00 0
7f29725fa000-7f29725fe000 ---p 00000000 00:00 0
7f29725fe000-7f29726fb000 rw-p 00000000 00:00 0
7f29726fb000-7f29726ff000 ---p 00000000 00:00 0
7f29726ff000-7f29727fc000 rw-p 00000000 00:00 0
7f29727fc000-7f2972800000 ---p 00000000 00:00 0
7f2972800000-7f29728fd000 rw-p 00000000 00:00 0
7f29728fd000-7f2972901000 ---p 00000000 00:00 0
7f2972901000-7f29729fe000 rw-p 00000000 00:00 0
7f29729fe000-7f2972a02000 ---p 00000000 00:00 0
7f2972a02000-7f2972aff000 rw-p 00000000 00:00 0
7f2972aff000-7f2972b03000 ---p 00000000 00:00 0
7f2972b03000-7f2973000000 rw-p 00000000 00:00 0
7f2973000000-7f2973400000 rw-p 00000000 00:00 0
7f29734bd000-7f29734c1000 ---p 00000000 00:00 0
7f29734c1000-7f297385d000 rw-p 00000000 00:00 0
7f297385d000-7f2974314000 ---p 00000000 00:00 0
7f2974314000-7f2974464000 rw-p 00000000 00:00 0
7f2974464000-7f29749be000 ---p 00000000 00:00 0
7f29749be000-7f2974c5d000 rw-p 00000000 00:00 0
7f2974c5d000-7f2975714000 ---p 00000000 00:00 0
7f2975714000-7f2975715000 rw-p 00000000 00:00 0
7f2975715000-7f2975985000 rwxp 00000000 00:00 0
7f2975985000-7f2975ca4000 ---p 00000000 00:00 0
7f2975ca4000-7f2976844000 rwxp 00000000 00:00 0
7f2976844000-7f297d1dc000 ---p 00000000 00:00 0
7f297d1dc000-7f297dd6c000 rwxp 00000000 00:00 0
7f297dd6c000-7f2984715000 ---p 00000000 00:00 0
7f2984715000-7f298c000000 r--s 00000000 00:34 6888076638 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/modules
7f298c000000-7f298d339000 rw-p 00000000 00:00 0
7f298d339000-7f2990000000 ---p 00000000 00:00 0
7f2990023000-7f2990030000 r-xp 00000000 00:34 6888076636 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libverify.so
7f2990030000-7f2990032000 r--p 0000c000 00:34 6888076636 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libverify.so
7f2990032000-7f2990033000 rw-p 0000e000 00:34 6888076636 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libverify.so
7f2990033000-7f2990037000 ---p 00000000 00:00 0
7f2990037000-7f2990134000 rw-p 00000000 00:00 0
7f2990134000-7f2990135000 ---p 00000000 00:00 0
7f2990135000-7f2990236000 rw-p 00000000 00:00 0
7f2990236000-7f2990304000 r-xp 00000000 00:34 6888076622 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjsvml.so
7f2990304000-7f2990305000 r--p 000cd000 00:34 6888076622 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjsvml.so
7f2990305000-7f2990306000 rw-p 000ce000 00:34 6888076622 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjsvml.so
7f2990306000-7f29903fa000 rw-p 00000000 00:00 0
7f29903fa000-7f29904cd000 ---p 00000000 00:00 0
7f29904cd000-7f29904e5000 rw-p 00000000 00:00 0
7f29904e5000-7f29905b8000 ---p 00000000 00:00 0
7f29905b8000-7f2990e8c000 r--s 00000000 fd:08 25175435 /var/lib/sss/mc/passwd
7f2990e8c000-7f2990e96000 r-xp 00000000 fd:00 101531284 /usr/lib64/libnss_sss.so.2
7f2990e96000-7f2991095000 ---p 0000a000 fd:00 101531284 /usr/lib64/libnss_sss.so.2
7f2991095000-7f2991096000 r--p 00009000 fd:00 101531284 /usr/lib64/libnss_sss.so.2
7f2991096000-7f2991097000 rw-p 0000a000 fd:00 101531284 /usr/lib64/libnss_sss.so.2
7f2991097000-7f2991218000 r-xp 00000000 fd:00 100669133 /usr/lib64/libm-2.28.so
7f2991218000-7f2991417000 ---p 00181000 fd:00 100669133 /usr/lib64/libm-2.28.so
7f2991417000-7f2991418000 r--p 00180000 fd:00 100669133 /usr/lib64/libm-2.28.so
7f2991418000-7f2991419000 rw-p 00181000 fd:00 100669133 /usr/lib64/libm-2.28.so
7f2991419000-7f2991420000 r-xp 00000000 fd:00 100669147 /usr/lib64/librt-2.28.so
7f2991420000-7f299161f000 ---p 00007000 fd:00 100669147 /usr/lib64/librt-2.28.so
7f299161f000-7f2991620000 r--p 00006000 fd:00 100669147 /usr/lib64/librt-2.28.so
7f2991620000-7f2991621000 rw-p 00007000 fd:00 100669147 /usr/lib64/librt-2.28.so
7f2991621000-7f299274b000 r-xp 00000000 00:34 6888076650 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so
7f299274b000-7f299274c000 ---p 0112a000 00:34 6888076650 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so
7f299274c000-7f2992801000 r--p 0112a000 00:34 6888076650 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so
7f2992801000-7f2992834000 rw-p 011df000 00:34 6888076650 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/server/libjvm.so
7f2992834000-7f299288e000 rw-p 00000000 00:00 0
7f299288e000-7f2992a47000 r-xp 00000000 fd:00 100669129 /usr/lib64/libc-2.28.so
7f2992a47000-7f2992c47000 ---p 001b9000 fd:00 100669129 /usr/lib64/libc-2.28.so
7f2992c47000-7f2992c4b000 r--p 001b9000 fd:00 100669129 /usr/lib64/libc-2.28.so
7f2992c4b000-7f2992c4d000 rw-p 001bd000 fd:00 100669129 /usr/lib64/libc-2.28.so
7f2992c4d000-7f2992c51000 rw-p 00000000 00:00 0
7f2992c51000-7f2992c54000 r-xp 00000000 fd:00 100669131 /usr/lib64/libdl-2.28.so
7f2992c54000-7f2992e53000 ---p 00003000 fd:00 100669131 /usr/lib64/libdl-2.28.so
7f2992e53000-7f2992e54000 r--p 00002000 fd:00 100669131 /usr/lib64/libdl-2.28.so
7f2992e54000-7f2992e55000 rw-p 00003000 fd:00 100669131 /usr/lib64/libdl-2.28.so
7f2992e55000-7f2992e70000 r-xp 00000000 fd:00 100669143 /usr/lib64/libpthread-2.28.so
7f2992e70000-7f299306f000 ---p 0001b000 fd:00 100669143 /usr/lib64/libpthread-2.28.so
7f299306f000-7f2993070000 r--p 0001a000 fd:00 100669143 /usr/lib64/libpthread-2.28.so
7f2993070000-7f2993071000 rw-p 0001b000 fd:00 100669143 /usr/lib64/libpthread-2.28.so
7f2993071000-7f2993075000 rw-p 00000000 00:00 0
7f2993075000-7f299308b000 r-xp 00000000 fd:00 100669282 /usr/lib64/libz.so.1.2.11
7f299308b000-7f299328a000 ---p 00016000 fd:00 100669282 /usr/lib64/libz.so.1.2.11
7f299328a000-7f299328b000 r--p 00015000 fd:00 100669282 /usr/lib64/libz.so.1.2.11
7f299328b000-7f299328c000 rw-p 00000000 00:00 0
7f299328c000-7f29932b5000 r-xp 00000000 fd:00 100669122 /usr/lib64/ld-2.28.so
7f29932b5000-7f29932b7000 r-xp 00000000 00:34 6888076606 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libextnet.so
7f29932b7000-7f29932b8000 r--p 00001000 00:34 6888076606 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libextnet.so
7f29932b8000-7f29932b9000 rw-p 00002000 00:34 6888076606 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libextnet.so
7f29932b9000-7f29932bf000 r-xp 00000000 00:34 6888076626 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement_ext.so
7f29932bf000-7f29932c0000 r--p 00005000 00:34 6888076626 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement_ext.so
7f29932c0000-7f29932c1000 rw-p 00006000 00:34 6888076626 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement_ext.so
7f29932c1000-7f29932c8000 r-xp 00000000 00:34 6888076637 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libzip.so
7f29932c8000-7f29932c9000 ---p 00007000 00:34 6888076637 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libzip.so
7f29932c9000-7f29932ca000 r--p 00007000 00:34 6888076637 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libzip.so
7f29932ca000-7f29932cb000 rw-p 00008000 00:34 6888076637 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libzip.so
7f29932cb000-7f29932e0000 r-xp 00000000 00:34 6888076628 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnet.so
7f29932e0000-7f29932e1000 ---p 00015000 00:34 6888076628 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnet.so
7f29932e1000-7f29932e2000 r--p 00015000 00:34 6888076628 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnet.so
7f29932e2000-7f29932e3000 rw-p 00016000 00:34 6888076628 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnet.so
7f29932e3000-7f29932f6000 r-xp 00000000 00:34 6888076629 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnio.so
7f29932f6000-7f29932f7000 r--p 00012000 00:34 6888076629 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnio.so
7f29932f7000-7f29932f8000 rw-p 00013000 00:34 6888076629 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libnio.so
7f29932f8000-7f299333e000 rw-p 00000000 00:00 0
7f299333e000-7f2993345000 ---p 00000000 00:00 0
7f2993345000-7f2993369000 r-xp 00000000 00:34 6888076613 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjava.so
7f2993369000-7f299336a000 ---p 00024000 00:34 6888076613 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjava.so
7f299336a000-7f299336b000 r--p 00024000 00:34 6888076613 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjava.so
7f299336b000-7f299336c000 rw-p 00025000 00:34 6888076613 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjava.so
7f299336c000-7f299336d000 rw-p 00000000 00:00 0
7f299336d000-7f2993388000 r-xp 00000000 00:34 6888076618 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjimage.so
7f2993388000-7f2993389000 ---p 0001b000 00:34 6888076618 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjimage.so
7f2993389000-7f299338b000 r--p 0001b000 00:34 6888076618 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjimage.so
7f299338b000-7f299338c000 rw-p 0001d000 00:34 6888076618 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjimage.so
7f299338c000-7f2993390000 ---p 00000000 00:00 0
7f2993390000-7f299348f000 rw-p 00000000 00:00 0
7f299348f000-7f299349e000 r-xp 00000000 00:34 6888076619 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjli.so
7f299349e000-7f299349f000 r--p 0000e000 00:34 6888076619 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjli.so
7f299349f000-7f29934a0000 rw-p 0000f000 00:34 6888076619 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libjli.so
7f29934a1000-7f29934a5000 r-xp 00000000 00:34 6888076624 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement.so
7f29934a5000-7f29934a6000 r--p 00003000 00:34 6888076624 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement.so
7f29934a6000-7f29934a7000 rw-p 00004000 00:34 6888076624 /gpfs/data/icelake-apps/compilers/openjdk/17.0.2/lib/libmanagement.so
7f29934a7000-7f29934af000 rw-s 00000000 fd:03 805316417 /tmp/hsperfdata_kmillan/20119
7f29934af000-7f29934b0000 ---p 00000000 00:00 0
7f29934b0000-7f29934b1000 r--p 00000000 00:00 0
7f29934b1000-7f29934b2000 ---p 00000000 00:00 0
7f29934b2000-7f29934b4000 rw-p 00000000 00:00 0
7f29934b4000-7f29934b5000 r--p 00028000 fd:00 100669122 /usr/lib64/ld-2.28.so
7f29934b5000-7f29934b6000 rw-p 00029000 fd:00 100669122 /usr/lib64/ld-2.28.so
7f29934b6000-7f29934b7000 rw-p 00000000 00:00 0
7ffd626ab000-7ffd626ce000 rw-p 00000000 00:00 0 [stack]
7ffd626d2000-7ffd626d5000 r--p 00000000 00:00 0 [vvar]
7ffd626d5000-7ffd626d7000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
VM Arguments:
jvm_args: -Xmx10G
java_command: /apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R /scratch/kmillan/WES/ref_genome/Homo_sapiens.GRCh38.dna.toplevel.fa -I Merged_S14.bam --pair-hmm-implementation LOGLESS_CACHING -O Merged_output_S14.vcf.gz -bamout Merged_aligned_output_S14.bam
java_class_path (initial): /apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar
Launcher Type: SUN_STANDARD
[Global flags]
intx CICompilerCount = 2 {product} {ergonomic}
size_t InitialHeapSize = 2107637760 {product} {ergonomic}
size_t MaxHeapSize = 10737418240 {product} {command line}
size_t MaxNewSize = 3579117568 {product} {ergonomic}
size_t MinHeapDeltaBytes = 196608 {product} {ergonomic}
size_t MinHeapSize = 8388608 {product} {ergonomic}
size_t NewSize = 702545920 {product} {ergonomic}
uintx NonNMethodCodeHeapSize = 5826188 {pd product} {ergonomic}
uintx NonProfiledCodeHeapSize = 122916026 {pd product} {ergonomic}
size_t OldSize = 1405091840 {product} {ergonomic}
uintx ProfiledCodeHeapSize = 122916026 {pd product} {ergonomic}
uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
bool SegmentedCodeCache = true {product} {ergonomic}
size_t SoftMaxHeapSize = 10737418240 {manageable} {ergonomic}
bool UseCompressedClassPointers = true {product lp64_product} {ergonomic}
bool UseCompressedOops = true {product lp64_product} {ergonomic}
bool UseSerialGC = true {product} {ergonomic}
Logging:
Log output configuration:
#0: stdout all=warning uptime,level,tags
#1: stderr all=off uptime,level,tags
Environment Variables:
JAVA_HOME=/apps/compilers/openjdk/17.0.2
CLASSPATH=/apps/software/openjdk-17.0.2/gatk/4.4.0.0/gatk-package-4.4.0.0-local.jar
PATH=/apps/software/openjdk-17.0.2/gatk/4.4.0.0:/apps/compilers/openjdk/17.0.2/bin:/home/kmillan/.local/bin:/home/kmillan/bin:/apps/default/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/phoenix-2.2.0/bin
LD_LIBRARY_PATH=/apps/default/lib:
SHELL=/bin/bash
LANG=en_US.UTF-8
LC_ALL=C
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:
Red Hat Enterprise Linux release 8.3 (Ootpa)
uname: Linux 4.18.0-240.22.1.el8_3.x86_64 #1 SMP Thu Mar 25 14:36:04 EDT 2021 x86_64
OS uptime: 10 days 5:16 hours
libc: glibc 2.28 NPTL 2.28
rlimit (soft/hard): STACK 8192k/infinity , CORE infinity/infinity , NPROC 513323/513323 , NOFILE 131072/131072 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity
load average: 4.00 4.01 4.25
/proc/meminfo:
MemTotal: 131618192 kB
MemFree: 44256272 kB
MemAvailable: 53478128 kB
Buffers: 32 kB
Cached: 9857884 kB
SwapCached: 39276 kB
Active: 62593688 kB
Inactive: 5290816 kB
Active(anon): 57623528 kB
Inactive(anon): 404236 kB
Active(file): 4970160 kB
Inactive(file): 4886580 kB
Unevictable: 16777216 kB
Mlocked: 16777216 kB
SwapTotal: 134217724 kB
SwapFree: 133810940 kB
Dirty: 20 kB
Writeback: 0 kB
AnonPages: 74709212 kB
Mapped: 763004 kB
Shmem: 1164 kB
KReclaimable: 326348 kB
Slab: 860568 kB
SReclaimable: 326348 kB
SUnreclaim: 534220 kB
KernelStack: 34992 kB
PageTables: 167972 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 200026820 kB
Committed_AS: 82144456 kB
VmallocTotal: 13743895347199 kB
VmallocUsed: 0 kB
VmallocChunk: 0 kB
Percpu: 105216 kB
HardwareCorrupted: 0 kB
AnonHugePages: 60641280 kB
ShmemHugePages: 0 kB
ShmemPmdMapped: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
Hugetlb: 0 kB
DirectMap4k: 423196 kB
DirectMap2M: 35885056 kB
DirectMap1G: 99614720 kB
/sys/kernel/mm/transparent_hugepage/enabled: [always] madvise never
/sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter): always defer defer+madvise [madvise] never
Process Memory:
Virtual Size: 13018724K (peak: 13022820K)
Resident Set Size: 2242772K (peak: 2252376K) (anon: 2205488K, file: 37284K, shmem: 0K)
Swapped out: 0K
C-Heap outstanding allocations: 26628K
/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 1026646
/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): 32768
container (cgroup) information:
container_type: cgroupv1
cpu_cpuset_cpus: 6
cpu_memory_nodes: 0-3
active_processor_count: 1
cpu_quota: no quota
cpu_period: 100000
cpu_shares: no shares
memory_limit_in_bytes: 134776619008
memory_and_swap_limit_in_bytes: 134776619008
memory_soft_limit_in_bytes: unlimited
memory_usage_in_bytes: 6855024640
memory_max_usage_in_bytes: 6860976128
Steal ticks since vm start: 0
Steal ticks percentage since vm start: 0.000
CPU: total 32 (initial active 1) (16 cores per cpu, 2 threads per core) family 6 model 106 stepping 6 microcode 0xd000331, 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, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, sha, fma, vzeroupper, avx512_vpopcntdq, avx512_vpclmulqdq, avx512_vaes, avx512_vnni, clflush, clflushopt, clwb, avx512_vbmi2, avx512_vbmi
CPU Model and flags from /proc/cpuinfo:
model name : Intel(R) Xeon(R) Gold 6326 CPU @ 2.90GHz
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 cpuid aperfmperf 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 cpuid_fault epb cat_l3 invpcid_single intel_ppin ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb intel_pt avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local split_lock_detect wbnoinvd dtherm ida arat pln pts hwp_epp avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg tme avx512_vpopcntdq la57 rdpid md_clear pconfig flush_l1d arch_capabilities
Online cpus: 0-31
Offline cpus:
BIOS frequency limitation: <Not Available>
Frequency switch latency (ns): <Not Available>
Available cpu frequencies: <Not Available>
Current governor: <Not Available>
Core performance/turbo boost: <Not Available>
Memory: 4k page, physical 131617792k(124923448k free), swap 134217724k(133810940k free)
Page Sizes: 4k
vm_info: OpenJDK 64-Bit Server VM (17.0.2+8-86) for linux-amd64 JRE (17.0.2+8-86), built on Dec 7 2021 21:41:21 by "mach5one" with gcc 10.3.0
END.
-
I also wanted to note that I used ValidateSamFile to see if there were errors in my bam files that could be causing this issue however no errors were found by the program.
-
Since my input bam files showed no errors I also ran ValidateSameFile on my output bam generated from HaplotypeCaller and received this error:
14:29:51.833 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/picard/3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
14:29:51.885 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/kmillan/libgkl_compression1287947824039740955.so: /tmp/kmillan/libgkl_compression1287947824039740955.so: failed to map segment from shared object)
14:29:51.885 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/picard/3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
14:29:51.890 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/kmillan/libgkl_compression4302086967116885162.so: /tmp/kmillan/libgkl_compression4302086967116885162.so: failed to map segment from shared object)
[Fri Dec 01 14:29:51 CST 2023] ValidateSamFile --INPUT Merged_aligned_output_S14.bam --MODE SUMMARY --REFERENCE_SEQUENCE /scratch/kmillan/WES/ref_genome/Homo_sapiens.GRCh38.dna.toplevel.fa --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Dec 01 14:29:51 CST 2023] Executing as kmillan@cri22cn002.cri.uchicago.edu on Linux 4.18.0-240.22.1.el8_3.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.2+8-86; Deflater: Jdk; Inflater: Jdk; Provider GCS is not available; Picard version: Version:3.0.0
14:29:52.186 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
WARNING: BAM index file /scratch/kmillan/WES/data/Merged_aligned_output_S14.bai is older than BAM /scratch/kmillan/WES/data/Merged_aligned_output_S14.bam
## HISTOGRAM java.lang.String
Error Type Count
ERROR:INVALID_INDEX_FILE_POINTER 1
ERROR:INVALID_TAG_NM 240996
ERROR:MATES_ARE_SAME_END 52573
ERROR:MATE_NOT_FOUND 571882
ERROR:MISMATCH_FLAG_MATE_NEG_STRAND 105016
ERROR:MISMATCH_FLAG_MATE_UNMAPPED 138
ERROR:MISMATCH_MATE_ALIGNMENT_START 450774
ERROR:MISMATCH_MATE_CIGAR_STRING 662869
ERROR:MISSING_PLATFORM_VALUE 1
ERROR:TRUNCATED_FILE 2
WARNING:MISSING_TAG_NM 134357
[Fri Dec 01 14:30:01 CST 2023] picard.sam.ValidateSamFile done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=2037383168According to this output, and the output from the scheduler (below) it seems that the code encounters an error at the -bamout flag. In my full script (including scheduler information), Line 24 is where I indicate the -bamout flag. Based on this information, and the reference to a problematic frame in the initial log posted above, I am wondering if this is a script issue or an issue with the program.
A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f2992158c7b, pid=20119, tid=20262
#
# JRE version: OpenJDK Runtime Environment (17.0.2+8) (build 17.0.2+8-86)
# Java VM: OpenJDK 64-Bit Server VM (17.0.2+8-86, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, serial gc, linux-amd64)
# Problematic frame:
# V [libjvm.so+0xb37c7b] markWord::displaced_mark_helper() const+0xb
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %e" (or dumping to /scratch/kmillan/WES/data/core.20119)
#
# An error report file with more information is saved as:
# /scratch/kmillan/WES/data/hs_err_pid20119.log
#
# If you would like to submit a bug report, please visit:
# https://bugreport.java.com/bugreport/crash.jsp
#
/var/spool/slurmd/job3303813/slurm_script: line 24: 20119 Aborted (core dumped) java -Xmx10G -jar ${GATK} HaplotypeCaller -R $ref -I Merged_S14.bam --pair-hmm-implementation LOGLESS_CACHING -O Merged_output_S14.vcf.gz -bamout Merged_aligned_output_S14.bam -
Hi Kaina Millan,
We have had reports from some users of problems like this with certain distributions of Java. If you're able, we recommend using the temurin-17-jdk distribution for Java 17 (or asking your IT department to install it). Instructions for installing it on Red Hat Linux are here: https://adoptium.net/installation/linux/
Alternatively (and much more simply), you can run GATK via the official docker image (https://hub.docker.com/r/broadinstitute/gatk/), which comes packaged with a working distribution of Java and everything else that GATK requires.
Another thing that appears to be going on here is that GATK is failing to load its native libraries:14:29:51.833 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/picard/3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
14:29:51.885 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/kmillan/libgkl_compression1287947824039740955.so: /tmp/kmillan/libgkl_compression1287947824039740955.so: failed to map segment from shared object)
14:29:51.885 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/icelake-apps/software/openjdk-17.0.2/picard/3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
14:29:51.890 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/kmillan/libgkl_compression4302086967116885162.so: /tmp/kmillan/libgkl_compression4302086967116885162.so: failed to map segment from shared object)
Your cluster may be set up to disallow loading executable code from the temp directory (/tmp/kmillan/). You can try providing a different temp directory when running GATK.
Hope this helps,David
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Hi David,
Thanks for providing these recommendations. I will give these a try and report back!
Kaina
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