# # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x0000003fd267c5ac, pid=23000, tid=1092311360 # # JRE version: 6.0_18-b07 # Java VM: Java HotSpot(TM) 64-Bit Server VM (16.0-b13 mixed mode linux-amd64 ) # Problematic frame: # C [libc.so.6+0x7c5ac] # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # --------------- T H R E A D --------------- Current thread (0x0000000051a90000): JavaThread "main" [_thread_in_vm, id=23063, stack(0x00000000410b5000,0x00000000411b6000)] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=2 (SEGV_ACCERR), si_addr=0x00002aaaaaf53ff8 Registers: RAX=0x00002aaaaaf54000, RBX=0x00002aab2b598088, RCX=0x1fffffffeff577f8, RDX=0x00002aaaaaf56cc0 RSP=0x00000000411b46c8, RBP=0x00002aaaab518070, RSI=0x00002aaaaaf53ff8, RDI=0x00002aab2afd4018 R8 =0x0000000000000000, R9 =0x000000008007fffc, R10=0x0000000000000000, R11=0x0000000000000018 R12=0x00002aabab518090, R13=0xffffffff8007fff8, R14=0x0000000000000000, R15=0x0000000000000000 RIP=0x0000003fd267c5ac, EFL=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000004 TRAPNO=0x000000000000000e Top of Stack: (sp=0x00000000411b46c8) 0x00000000411b46c8: 0000003fd267a9d1 0000000000000000 0x00000000411b46d8: 0000000000001803 00000000411b4720 0x00000000411b46e8: 0000000000000000 0000000000000000 0x00000000411b46f8: 00002b7c9ff13fc5 0000000051a8eef0 0x00000000411b4708: 0000000051a90000 00002b7ca0140530 0x00000000411b4718: 00000000411b47b8 00000000411b4790 0x00000000411b4728: 00002b7c9fc6d9fd 0000000051a90000 0x00000000411b4738: 0000000051a90bb8 0000000051a90000 0x00000000411b4748: 00002b7ca0140530 0000000051a90000 0x00000000411b4758: 00002b7c9fa19abc 0000000020000003 0x00000000411b4768: 00002aaaae04ea48 0000000051a90000 0x00000000411b4778: 00000000411b4808 00000000411b47d8 0x00000000411b4788: 0000000051a90000 00000000411b47f0 0x00000000411b4798: 00002aaaaafbf629 000000004003fffe 0x00000000411b47a8: 00002aab2b498060 00000000411b47b0 0x00000000411b47b8: 00002aabab518078 00000000411b4808 0x00000000411b47c8: 00002aaaae14e9a0 0000000000000000 0x00000000411b47d8: 00002aaaae050448 0000000000000000 0x00000000411b47e8: 00000000411b4800 00000000411b4870 0x00000000411b47f8: 00002aaaaaf5da42 00002aaaaaf5da42 0x00000000411b4808: 000000004003fffe 0000000000000000 0x00000000411b4818: 00002aabab518078 0000000000000000 0x00000000411b4828: 00002aab2b498060 00000000411b4830 0x00000000411b4838: 00002aaaae146ed6 00000000411b4890 0x00000000411b4848: 00002aaaae149bd0 0000000000000000 0x00000000411b4858: 00002aaaae146ee8 00000000411b4808 0x00000000411b4868: 00000000411b4888 00000000411b48e0 0x00000000411b4878: 00002aaaaaf5d8e9 00002aabab518078 0x00000000411b4888: 000000007fffffff 00002aab2b498060 0x00000000411b4898: 00002aad4846caf8 00000000411b48a0 0x00000000411b48a8: 00002aaaae0a3b39 00000000411b4900 0x00000000411b48b8: 00002aaaae14f488 0000000000000000 Instructions: (pc=0x0000003fd267c5ac) 0x0000003fd267c59c: 48 8b 56 10 48 89 47 10 48 8b 46 08 48 89 57 08 0x0000003fd267c5ac: 48 8b 16 48 89 07 48 83 ef 40 48 83 e9 08 75 b4 Stack: [0x00000000410b5000,0x00000000411b6000], sp=0x00000000411b46c8, free space=3fd0000000000000018k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) C [libc.so.6+0x7c5ac] Java frames: (J=compiled Java code, j=interpreted, Vv=VM code) J java.lang.System.arraycopy(Ljava/lang/Object;ILjava/lang/Object;II)V j java.util.Arrays.copyOf([CI)[C+14 j java.lang.AbstractStringBuilder.expandCapacity(I)V+33 J java.lang.StringBuffer.append([CII)Ljava/lang/StringBuffer; J java.io.BufferedReader.readLine(Z)Ljava/lang/String; j java.io.BufferedReader.readLine()Ljava/lang/String;+2 j NLJoin.runMatch(II[I[ILjava/lang/String;)Z+52 j NLJoin.main([Ljava/lang/String;)V+129 v ~StubRoutines::call_stub --------------- P R O C E S S --------------- Java Threads: ( => current thread ) 0x0000000051b28000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=23497, stack(0x00000000417e6000,0x00000000418e7000)] 0x0000000051b26000 JavaThread "CompilerThread1" daemon [_thread_blocked, id=23496, stack(0x00000000411b6000,0x00000000412b7000)] 0x0000000051b21000 JavaThread "CompilerThread0" daemon [_thread_blocked, id=23494, stack(0x0000000040f45000,0x0000000041046000)] 0x0000000051b1f000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=23487, stack(0x00000000404f8000,0x00000000405f9000)] 0x0000000051afa000 JavaThread "Finalizer" daemon [_thread_blocked, id=23441, stack(0x0000000042552000,0x0000000042653000)] 0x0000000051af8000 JavaThread "Reference Handler" daemon [_thread_blocked, id=23432, stack(0x0000000041cd6000,0x0000000041dd7000)] =>0x0000000051a90000 JavaThread "main" [_thread_in_vm, id=23063, stack(0x00000000410b5000,0x00000000411b6000)] Other Threads: 0x0000000051af3800 VMThread [stack: 0x0000000041bd5000,0x0000000041cd6000] [id=23423] 0x0000000051b2b000 WatcherThread [stack: 0x00000000418e7000,0x00000000419e8000] [id=23499] VM state:not at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: None Heap PSYoungGen total 296128K, used 142240K [0x00002aad48420000, 0x00002aad5ce90000, 0x00002aae92c20000) eden space 253888K, 56% used [0x00002aad48420000,0x00002aad50f08218,0x00002aad57c10000) from space 42240K, 0% used [0x00002aad5a550000,0x00002aad5a550000,0x00002aad5ce90000) to space 42240K, 0% used [0x00002aad57c10000,0x00002aad57c10000,0x00002aad5a550000) PSOldGen total 8542336K, used 8258528K [0x00002aaab3420000, 0x00002aacbca40000, 0x00002aad48420000) object space 8542336K, 96% used [0x00002aaab3420000,0x00002aacab518090,0x00002aacbca40000) PSPermGen total 21248K, used 2548K [0x00002aaaae020000, 0x00002aaaaf4e0000, 0x00002aaab3420000) object space 21248K, 11% used [0x00002aaaae020000,0x00002aaaae29d1b0,0x00002aaaaf4e0000) Dynamic libraries: 40000000-40009000 r-xp 00000000 00:2f 45447829 /gsc/software/linux-x86_64/jdk1.6.0_18/bin/java 40108000-4010a000 rwxp 00008000 00:2f 45447829 /gsc/software/linux-x86_64/jdk1.6.0_18/bin/java 404f8000-404fb000 ---p 404f8000 00:00 0 404fb000-405f9000 rwxp 404fb000 00:00 0 40f45000-40f48000 ---p 40f45000 00:00 0 40f48000-41046000 rwxp 40f48000 00:00 0 410b5000-410b8000 ---p 410b5000 00:00 0 410b8000-411b6000 rwxp 410b8000 00:00 0 411b6000-411b9000 ---p 411b6000 00:00 0 411b9000-412b7000 rwxp 411b9000 00:00 0 417e6000-417e9000 ---p 417e6000 00:00 0 417e9000-418e7000 rwxp 417e9000 00:00 0 418e7000-418e8000 ---p 418e7000 00:00 0 418e8000-419e8000 rwxp 418e8000 00:00 0 41ad4000-41ad5000 ---p 41ad4000 00:00 0 41ad5000-41bd5000 rwxp 41ad5000 00:00 0 41bd5000-41bd6000 ---p 41bd5000 00:00 0 41bd6000-41cd6000 rwxp 41bd6000 00:00 0 41cd6000-41cd9000 ---p 41cd6000 00:00 0 41cd9000-41dd7000 rwxp 41cd9000 00:00 0 41e4b000-41e4c000 ---p 41e4b000 00:00 0 41e4c000-41f4c000 rwxp 41e4c000 00:00 0 41f4c000-41f4d000 ---p 41f4c000 00:00 0 41f4d000-4204d000 rwxp 41f4d000 00:00 0 4204d000-4204e000 ---p 4204d000 00:00 0 4204e000-4214e000 rwxp 4204e000 00:00 0 4214e000-4214f000 ---p 4214e000 00:00 0 4214f000-4224f000 rwxp 4214f000 00:00 0 4224f000-42250000 ---p 4224f000 00:00 0 42250000-42350000 rwxp 42250000 00:00 0 42350000-42351000 ---p 42350000 00:00 0 42351000-42451000 rwxp 42351000 00:00 0 42451000-42452000 ---p 42451000 00:00 0 42452000-42552000 rwxp 42452000 00:00 0 42552000-42555000 ---p 42552000 00:00 0 42555000-42653000 rwxp 42555000 00:00 0 51a89000-51ddb000 rwxp 51a89000 00:00 0 [heap] 3fd2200000-3fd221c000 r-xp 00000000 68:11 425995 /lib64/ld-2.5.so 3fd241b000-3fd241c000 r-xp 0001b000 68:11 425995 /lib64/ld-2.5.so 3fd241c000-3fd241d000 rwxp 0001c000 68:11 425995 /lib64/ld-2.5.so 3fd2600000-3fd274e000 r-xp 00000000 68:11 425999 /lib64/libc-2.5.so 3fd274e000-3fd294d000 ---p 0014e000 68:11 425999 /lib64/libc-2.5.so 3fd294d000-3fd2951000 r-xp 0014d000 68:11 425999 /lib64/libc-2.5.so 3fd2951000-3fd2952000 rwxp 00151000 68:11 425999 /lib64/libc-2.5.so 3fd2952000-3fd2957000 rwxp 3fd2952000 00:00 0 3fd2a00000-3fd2a02000 r-xp 00000000 68:11 426001 /lib64/libdl-2.5.so 3fd2a02000-3fd2c02000 ---p 00002000 68:11 426001 /lib64/libdl-2.5.so 3fd2c02000-3fd2c03000 r-xp 00002000 68:11 426001 /lib64/libdl-2.5.so 3fd2c03000-3fd2c04000 rwxp 00003000 68:11 426001 /lib64/libdl-2.5.so 3fd2e00000-3fd2e16000 r-xp 00000000 68:11 426011 /lib64/libpthread-2.5.so 3fd2e16000-3fd3015000 ---p 00016000 68:11 426011 /lib64/libpthread-2.5.so 3fd3015000-3fd3016000 r-xp 00015000 68:11 426011 /lib64/libpthread-2.5.so 3fd3016000-3fd3017000 rwxp 00016000 68:11 426011 /lib64/libpthread-2.5.so 3fd3017000-3fd301b000 rwxp 3fd3017000 00:00 0 3fd3200000-3fd3282000 r-xp 00000000 68:11 426015 /lib64/libm-2.5.so 3fd3282000-3fd3481000 ---p 00082000 68:11 426015 /lib64/libm-2.5.so 3fd3481000-3fd3482000 r-xp 00081000 68:11 426015 /lib64/libm-2.5.so 3fd3482000-3fd3483000 rwxp 00082000 68:11 426015 /lib64/libm-2.5.so 3fd3a00000-3fd3a07000 r-xp 00000000 68:11 426019 /lib64/librt-2.5.so 3fd3a07000-3fd3c07000 ---p 00007000 68:11 426019 /lib64/librt-2.5.so 3fd3c07000-3fd3c08000 r-xp 00007000 68:11 426019 /lib64/librt-2.5.so 3fd3c08000-3fd3c09000 rwxp 00008000 68:11 426019 /lib64/librt-2.5.so 3fd5a00000-3fd5a15000 r-xp 00000000 68:11 426197 /lib64/libnsl-2.5.so 3fd5a15000-3fd5c14000 ---p 00015000 68:11 426197 /lib64/libnsl-2.5.so 3fd5c14000-3fd5c15000 r-xp 00014000 68:11 426197 /lib64/libnsl-2.5.so 3fd5c15000-3fd5c16000 rwxp 00015000 68:11 426197 /lib64/libnsl-2.5.so 3fd5c16000-3fd5c18000 rwxp 3fd5c16000 00:00 0 2aaaaaabc000-2aaaaaac9000 r-xp 00000000 00:2f 67265981 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libverify.so 2aaaaaac9000-2aaaaabc8000 ---p 0000d000 00:2f 67265981 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libverify.so 2aaaaabc8000-2aaaaabcb000 rwxp 0000c000 00:2f 67265981 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libverify.so 2aaaaabcb000-2aaaaabf4000 r-xp 00000000 00:2f 31140623 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libjava.so 2aaaaabf4000-2aaaaacf3000 ---p 00029000 00:2f 31140623 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libjava.so 2aaaaacf3000-2aaaaacfa000 rwxp 00028000 00:2f 31140623 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libjava.so 2aaaaacfa000-2aaaaacfb000 r-xp 2aaaaacfa000 00:00 0 2aaaaacfb000-2aaaaacfc000 rwxp 2aaaaacfb000 00:00 0 2aaaaacfc000-2aaaaad03000 r-xp 00000000 00:2f 31140612 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/native_threads/libhpi.so 2aaaaad03000-2aaaaae04000 ---p 00007000 00:2f 31140612 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/native_threads/libhpi.so 2aaaaae04000-2aaaaae06000 rwxp 00008000 00:2f 31140612 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/native_threads/libhpi.so 2aaaaae06000-2aaaaae07000 rwxp 2aaaaae06000 00:00 0 2aaaaae07000-2aaaaae3c000 r-xs 00000000 68:13 66846762 /var/run/nscd/db8SK7wg (deleted) 2aaaaae3c000-2aaaaae44000 rwxs 00000000 68:11 233408 /tmp/hsperfdata_omorozova/23000 2aaaaae44000-2aaaaae52000 r-xp 00000000 00:2f 31140610 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libzip.so 2aaaaae52000-2aaaaaf54000 ---p 0000e000 00:2f 31140610 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libzip.so 2aaaaaf54000-2aaaaaf57000 rwxp 00010000 00:2f 31140610 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/libzip.so 2aaaaaf57000-2aaaab1c8000 rwxp 2aaaaaf57000 00:00 0 2aaaab1c8000-2aaaadf58000 rwxp 2aaaab1c8000 00:00 0 2aaaadf58000-2aaaadf62000 rwxp 2aaaadf58000 00:00 0 2aaaadf62000-2aaaae018000 rwxp 2aaaadf62000 00:00 0 2aaaae020000-2aaaaf4e0000 rwxp 2aaaae020000 00:00 0 2aaaaf4e0000-2aaab3420000 rwxp 2aaaaf4e0000 00:00 0 2aaab3420000-2aacbca40000 rwxp 2aaab3420000 00:00 0 2aacbca40000-2aad48420000 rwxp 2aacbca40000 00:00 0 2aad48420000-2aad5ce90000 rwxp 2aad48420000 00:00 0 2aad5ce90000-2aae92c20000 rwxp 2aad5ce90000 00:00 0 2aae92c20000-2aae92c2b000 rwxp 2aae92c20000 00:00 0 2aae92c2b000-2aae92c4a000 rwxp 2aae92c2b000 00:00 0 2aae92c4a000-2aae93c96000 rwxp 2aae92c4a000 00:00 0 2aae93c96000-2aae940f2000 rwxp 2aae93c96000 00:00 0 2aae940f2000-2aae94198000 rwxp 2aae940f2000 00:00 0 2aae94198000-2aae94b46000 rwxp 2aae94198000 00:00 0 2aae94b46000-2aae95b93000 rwxp 2aae94b46000 00:00 0 2aae95b93000-2aae95fef000 rwxp 2aae95b93000 00:00 0 2aae95fef000-2aae95ffa000 rwxp 2aae95fef000 00:00 0 2aae95ffa000-2aae96019000 rwxp 2aae95ffa000 00:00 0 2aae96019000-2aae96041000 rwxp 2aae96019000 00:00 0 2aae96041000-2aae961d7000 r-xs 02fc6000 00:2f 388247 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/rt.jar 2aae961d7000-2aae96b13000 rwxp 2aae961d7000 00:00 0 2aae96b13000-2aae9a0e9000 r-xp 00000000 68:11 871056 /usr/lib/locale/locale-archive 2b7c9f711000-2b7c9f713000 rwxp 2b7c9f711000 00:00 0 2b7c9f723000-2b7c9f72a000 r-xp 00000000 00:2f 67265971 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/jli/libjli.so 2b7c9f72a000-2b7c9f82b000 ---p 00007000 00:2f 67265971 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/jli/libjli.so 2b7c9f82b000-2b7c9f82d000 rwxp 00008000 00:2f 67265971 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/jli/libjli.so 2b7c9f82d000-2b7c9f82f000 rwxp 2b7c9f82d000 00:00 0 2b7c9f82f000-2b7c9ffe3000 r-xp 00000000 00:2f 18666105 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/server/libjvm.so 2b7c9ffe3000-2b7ca00e3000 ---p 007b4000 00:2f 18666105 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/server/libjvm.so 2b7ca00e3000-2b7ca026d000 rwxp 007b4000 00:2f 18666105 /gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/server/libjvm.so 2b7ca026d000-2b7ca02a6000 rwxp 2b7ca026d000 00:00 0 7fff949b9000-7fff949ce000 rwxp 7ffffffea000 00:00 0 [stack] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] VM Arguments: java_command: NLJoin /projects/olenaprj/resources/FUBP1.lookup.extended HS1894_3_lanes.pileup Launcher Type: SUN_STANDARD Environment Variables: JAVA_HOME=/gsc/software/linux-x86_64/jdk1.6.0_18 PATH=/home/rmorin/samtools/misc:/home/rmorin/samtools:/home/rmorin/novo/novocraft/:/home/rmorin/svn/working_copy/wtss:/home/rmorin/svn/working_copy/general:/home/rmorin/soap/soap_1.10:/projects/rmorin/miRNA/mirdeep/miRDeep/:/home/rmorin/svn/working_copy/mirna/pipeline/:/home/rmorin/bin/perl/:/home/rmorin/bin/mfold_util/bin/:/home/rmorin/bin/mfold/bin/:/home/pubseq/BioSw/ViennaRNA/1.6.1/bin/:/home/pubseq/BioSw/Solexa/current/Eland:/home/rmorin/bin/bin:/var/opt/sge/bin/glinux/:/home/rmorin/lib/nsp-v0.71/Measures:.:/usr/bin/xemacs/bin:/usr/local/web/ActivePython-2.1/bin:/opt/bin/:/usr/xpg4/bin:/opt/csw/bin:/home/rmorin/myrna/scripts/:/usr/bin/:/home/pubseq/BioSw/BLAST2/current/bin/:/bin/:/usr/local/bin:/usr/bin/:/gsc/software/linux-x86_64/jdk1.6.0_18/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin LD_LIBRARY_PATH=/gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64/server:/gsc/software/linux-x86_64/jdk1.6.0_18/jre/lib/amd64:/gsc/software/linux-x86_64/jdk1.6.0_18/jre/../lib/amd64::/home/rmorin/lib/lib:/opt/mpiJava/lib:/opt/sge/lib/lx26-amd64:/home/rmorin/lib/zlib/zlib-1.2.3 SHELL=/bin/bash Signal Handlers: SIGSEGV: [libjvm.so+0x70f1a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x70f1a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x5da790], sa_mask[0]=0x00000000, sa_flags=0x10000004 SIGHUP: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGINT: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGTERM: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:CentOS release 5.5 (Final) uname:Linux 2.6.18-194.3.1.el5 #1 SMP Thu May 13 13:08:30 EDT 2010 x86_64 libc:glibc 2.5 NPTL 2.5 rlimit: STACK 10240k, CORE 0k, NPROC 522239, NOFILE 8192, AS infinity load average:34.90 38.62 39.67 CPU:total 8 (4 cores per cpu, 1 threads per core) family 6 model 23 stepping 6, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1 Memory: 4k page, physical 64974044k(300588k free), swap 102048268k(53756088k free) vm_info: Java HotSpot(TM) 64-Bit Server VM (16.0-b13) for linux-amd64 JRE (1.6.0_18-b07), built on Dec 17 2009 13:42:22 by "java_re" with gcc 3.2.2 (SuSE Linux) time: Sun Aug 14 14:53:45 2011 elapsed time: 3178 seconds