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nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
Apache License 2.0
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Unexpected JRE crash mid run. #403

Closed sylvinite closed 7 years ago

sylvinite commented 7 years ago

Our pipeline crashed due to a JRE error mid run. Resuming the run afterwards let the pipeline finish. This problem has not been reproducible. In case more information is necessary about the pipeline itself, it can be found at https://github.com/SciLifeLab/NGI-RNAseq .

Crash log:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  
[error occurred during error reporting (printing exception/signal name), id 0x7]

, pid=14926, tid=47027438065408
#
# JRE version: 7.0_25-b15
# Java VM: Java HotSpot(TM) 64-Bit Server VM (23.25-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# 
[error occurred during error reporting (printing problematic frame), id 0x7]

# Core dump written. Default location: /lupus/proj/ngi2016003/nobackup/NGI/ANALYSIS/P7709/rnaseq_ngi/core or core.14926 (max size 10 kB). To ensure a full core dump, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x00002ac524942800):  JavaThread "Thread-2" [_thread_in_native, id=21214, stack(0x00002ac56dad9000,0x00002ac56dbda000)]

siginfo:
[error occurred during error reporting (printing siginfo), id 0x7]

Registers:
RAX=0x00002ac5229ee668, RBX=0x00002ac5229ee8c8, RCX=0x0000000000000006, RDX=0x0000000000000052
RSP=0x00002ac56dbd62f0, RBP=0x0000000000000000, RSI=0x00000000d85191ac, RDI=0x00002ac52400f610
R8 =0x000000000000002c, R9 =0x0000000003614646, R10=0x00002ac52400f998, R11=0x00002ac56dbd6430
R12=0x0000000000000009, R13=0x00000000d85191ac, R14=0x00002ac52400fbc0, R15=0x0000000000000000
RIP=0x00002ac520362741, EFLAGS=0x0000000000010206, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00002ac56dbd62f0)
0x00002ac56dbd62f0:   00002ac528b2de9f 00002ac56dbd6330
0x00002ac56dbd6300:   00002ac56dbd6330 00002ac521010000
0x00002ac56dbd6310:   00002ac56dbd6440 00002ac528b2dd80
0x00002ac56dbd6320:   00002ac528b2e300 00002ac528b2dd80
0x00002ac56dbd6330:   0000000000000000 0000000000000000
0x00002ac56dbd6340:   00002ac52400f610 00002ac5d800ca90
0x00002ac56dbd6350:   00002ac5229ef318 0000000000000000
0x00002ac56dbd6360:   0000000200000000 0000000028b2e305
0x00002ac56dbd6370:   00002ac524007c90 00002ac56dbd6520
0x00002ac56dbd6380:   00002ac56dbd64d0 0000000000000000
0x00002ac56dbd6390:   0000000000000000 00002ac52400f998
0x00002ac56dbd63a0:   00002ac52400f610 00002ac52036301f
0x00002ac56dbd63b0:   0000000000000000 0000000000000000
0x00002ac56dbd63c0:   00002ac500000002 0000000000000000
0x00002ac56dbd63d0:   00002ac500000000 00002ac52400f610
0x00002ac56dbd63e0:   00002ac56dbd6af0 00002ac5217432b6
0x00002ac56dbd63f0:   00002ac5287b4b90 00002ac524942800
0x00002ac56dbd6400:   00002ac56dbd89d8 00002ac52400f998
0x00002ac56dbd6410:   00002ac56dbd6440 00002ac56dbd6430
0x00002ac56dbd6420:   00000000d85191ac 00002ac5d800ca90
0x00002ac56dbd6430:   00000000ffffffff 00002ac5b001b408
0x00002ac56dbd6440:   0000000000000000 0000000000000000
0x00002ac56dbd6450:   00002ac528b2db90 00002ac500000000
0x00002ac56dbd6460:   00002ac56dbd7be8 00002ac56dbd6de0
0x00002ac56dbd6470:   00002ac524942800 00002ac5287ae934
0x00002ac56dbd6480:   00002ac56dbd7be8 00002ac5289980ac
0x00002ac56dbd6490:   00000007b07c69a8 00000007b084a470
0x00002ac56dbd64a0:   00000007bb030560 00002ac520579c20
0x00002ac56dbd64b0:   00002ac52057a000 00000000012c4570
0x00002ac56dbd64c0:   00000000012c4570 00002ac5216b2f6d
0x00002ac56dbd64d0:   00002ac56dbd65b0 00002ac520ce53a9
0x00002ac56dbd64e0:   00002ac500000002 0000000000000000 

Instructions: (pc=0x00002ac520362741)
0x00002ac520362721:   40 08 48 89 44 24 60 48 8b 87 f8 02 00 00 48 85
0x00002ac520362731:   c0 0f 84 24 06 00 00 44 89 c9 23 8f f0 02 00 00
0x00002ac520362741:   48 8b 34 c8 8b 8f f4 02 00 00 4c 89 e8 48 d3 e8
0x00002ac520362751:   48 89 c1 48 89 f0 48 d3 e8 44 89 c1 48 d3 ee 48 

Register to memory mapping:

RAX=
[error occurred during error reporting (printing register info), id 0x7]

Stack: [0x00002ac56dad9000,0x00002ac56dbda000],  sp=0x00002ac56dbd62f0,  free space=1012k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)

[error occurred during error reporting (printing native stack), id 0x7]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  java.lang.ClassLoader$NativeLibrary.find(Ljava/lang/String;)J+0
j  java.lang.ClassLoader.findNative(Ljava/lang/ClassLoader;Ljava/lang/String;)J+49
v  ~StubRoutines::call_stub
j  sun.nio.fs.UnixNativeDispatcher.strerror(I)[B+0
J  sun.nio.fs.UnixException.translateToIOException(Ljava/lang/String;Ljava/lang/String;)Ljava/io/IOException;
J  sun.nio.fs.UnixException.rethrowAsIOException(Lsun/nio/fs/UnixPath;Lsun/nio/fs/UnixPath;)V
J  sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes()Ljava/nio/file/attribute/BasicFileAttributes;
J  sun.nio.fs.UnixFileSystemProvider.readAttributes(Ljava/nio/file/Path;Ljava/lang/Class;[Ljava/nio/file/LinkOption;)Ljava/nio/file/attribute/BasicFileAttributes;
J  sun.nio.fs.LinuxFileSystemProvider.readAttributes(Ljava/nio/file/Path;Ljava/lang/Class;[Ljava/nio/file/LinkOption;)Ljava/nio/file/attribute/BasicFileAttributes;
J  nextflow.file.FileHelper.readAttributes(Ljava/nio/file/Path;[Ljava/nio/file/LinkOption;)Ljava/nio/file/attribute/BasicFileAttributes;
J  sun.reflect.GeneratedMethodAccessor483.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.reflection.CachedMethod.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  groovy.lang.MetaMethod.doMethodInvoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.call(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;
J  nextflow.executor.GridTaskHandler.readExitStatus()Ljava/lang/Integer;
J  nextflow.executor.GridTaskHandler.checkIfCompleted()Z
J  nextflow.processor.TaskPollingMonitor.checkTaskStatus(Lnextflow/processor/TaskHandler;)V
J  nextflow.processor.TaskPollingMonitor.checkAllTasks()V
j  nextflow.processor.TaskPollingMonitor.pollLoop()V+73
v  ~StubRoutines::call_stub
J  sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.reflection.CachedMethod.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  groovy.lang.MetaMethod.doMethodInvoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;
J  groovy.lang.MetaClassImpl.invokeMethod(Ljava/lang/Class;Ljava/lang/Object;Ljava/lang/String;[Ljava/lang/Object;ZZ)Ljava/lang/Object;
J  groovy.lang.MetaClassImpl.invokeMethod(Ljava/lang/Object;Ljava/lang/String;[Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(Ljava/lang/Object;Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/Object;
J  org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(Ljava/lang/Object;Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/Object;
j  org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(Ljava/lang/Object;Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/Object;+7
j  nextflow.processor.TaskPollingMonitor$_start_closure6.doCall(Ljava/lang/Object;)Ljava/lang/Object;+13
j  nextflow.processor.TaskPollingMonitor$_start_closure6.call()Ljava/lang/Object;+2
j  groovy.lang.Closure.run()V+1
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00002ac5d800a000 JavaThread "process reaper" daemon [_thread_blocked, id=13384, stack(0x00002ac56f7f6000,0x00002ac56f81e000)]
  0x00002ac5d8012000 JavaThread "Actor Thread 306" daemon [_thread_blocked, id=25151, stack(0x00002ac56d9d8000,0x00002ac56dad9000)]
  0x00002ac5d800e800 JavaThread "pool-2-thread-1" [_thread_blocked, id=12717, stack(0x00002ac56eae9000,0x00002ac56ebea000)]
  0x00002ac60c004800 JavaThread "Actor Thread 284" daemon [_thread_blocked, id=17160, stack(0x00002ac56dddc000,0x00002ac56dedd000)]
  0x00002ac5249d6000 JavaThread "Thread-3" [_thread_blocked, id=21697, stack(0x00002ac56f6f5000,0x00002ac56f7f6000)]
=>0x00002ac524942800 JavaThread "Thread-2" [_thread_in_native, id=21214, stack(0x00002ac56dad9000,0x00002ac56dbda000)]
  0x00002ac52411f000 JavaThread "Service Thread" daemon [_thread_blocked, id=15217, stack(0x00002ac56c707000,0x00002ac56c808000)]
  0x00002ac52411c800 JavaThread "C1 CompilerThread11" daemon [_thread_blocked, id=15216, stack(0x00002ac56c606000,0x00002ac56c707000)]
  0x00002ac52411a800 JavaThread "C1 CompilerThread10" daemon [_thread_blocked, id=15215, stack(0x00002ac56c505000,0x00002ac56c606000)]
  0x00002ac524118000 JavaThread "C1 CompilerThread9" daemon [_thread_blocked, id=15214, stack(0x00002ac56c404000,0x00002ac56c505000)]
  0x00002ac524115800 JavaThread "C1 CompilerThread8" daemon [_thread_blocked, id=15213, stack(0x00002ac56c303000,0x00002ac56c404000)]
  0x00002ac524113800 JavaThread "C2 CompilerThread7" daemon [_thread_blocked, id=15212, stack(0x00002ac56c202000,0x00002ac56c303000)]
  0x00002ac524111000 JavaThread "C2 CompilerThread6" daemon [_thread_blocked, id=15211, stack(0x00002ac56c101000,0x00002ac56c202000)]
  0x00002ac52410f000 JavaThread "C2 CompilerThread5" daemon [_thread_blocked, id=15210, stack(0x00002ac56c000000,0x00002ac56c101000)]
  0x00002ac52410c800 JavaThread "C2 CompilerThread4" daemon [_thread_blocked, id=15209, stack(0x00002ac537e87000,0x00002ac537f88000)]
  0x00002ac52410a800 JavaThread "C2 CompilerThread3" daemon [_thread_blocked, id=15208, stack(0x00002ac537d86000,0x00002ac537e87000)]
  0x00002ac524108000 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=15207, stack(0x00002ac537c85000,0x00002ac537d86000)]
  0x00002ac524106000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=15204, stack(0x00002ac537b84000,0x00002ac537c85000)]
  0x00002ac524103000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=15203, stack(0x00002ac537a83000,0x00002ac537b84000)]
  0x00002ac524101000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=15202, stack(0x00002ac537982000,0x00002ac537a83000)]
  0x00002ac5240b2800 JavaThread "Finalizer" daemon [_thread_blocked, id=15063, stack(0x00002ac537881000,0x00002ac537982000)]
  0x00002ac5240b0000 JavaThread "Reference Handler" daemon [_thread_blocked, id=15060, stack(0x00002ac537780000,0x00002ac537881000)]
  0x00002ac52400b000 JavaThread "main" [_thread_blocked, id=15018, stack(0x00002ac520397000,0x00002ac520498000)]

Other Threads:
  0x00002ac5240a8800 VMThread [stack: 0x00002ac53767f000,0x00002ac537780000] [id=15050]
  0x00002ac52412a000 WatcherThread [stack: 0x00002ac56c808000,0x00002ac56c909000] [id=15220]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
 PSYoungGen      total 305856K, used 120850K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 36% used [0x00000007aaab0000,0x00000007b08f60d8,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007baac0000,0x00000007bc27ea68,0x00000007bd560000)
  to   space 36416K, 0% used [0x00000007bdc70000,0x00000007bdc70000,0x00000007c0000000)
 ParOldGen       total 699072K, used 104K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070001a000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26230K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc79d9e0,0x00000006fc7a0000)

Card table byte_map: [0x00002ac522d89000,0x00002ac5235b3000] byte_map_base: 0x00002ac51f5b2000

Polling page: 0x00002ac52037c000

Code Cache  [0x00002ac528000000, 0x00002ac528dc0000, 0x00002ac52e000000)
 total_blobs=5520 nmethods=4941 adapters=506 free_code_cache=84281Kb largest_free_block=86282944

Compilation events (10 events):
Event: 13823.772 Thread 0x00002ac52411a800 5090   !   1       sun.reflect.GeneratedMethodAccessor500::invoke (61 bytes)
Event: 13824.529 Thread 0x00002ac52411a800 nmethod 5090 0x00002ac528db4d90 code [0x00002ac528db4f40, 0x00002ac528db5348]
Event: 16689.293 Thread 0x00002ac524118000 5091       1       org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction::<init> (35 bytes)
Event: 16689.293 Thread 0x00002ac524115800 5092       1       sun.nio.fs.NativeBuffer$Deallocator::<init> (10 bytes)
Event: 16689.332 Thread 0x00002ac524115800 nmethod 5092 0x00002ac528db55d0 code [0x00002ac528db5720, 0x00002ac528db5870]
Event: 16689.332 Thread 0x00002ac524118000 nmethod 5091 0x00002ac528db58d0 code [0x00002ac528db5a60, 0x00002ac528db5ca8]
Event: 17264.349 Thread 0x00002ac52411a800 5093       1       com.esotericsoftware.kryo.serializers.CollectionSerializer::write (11 bytes)
Event: 17264.349 Thread 0x00002ac52411c800 5094       1       com.esotericsoftware.kryo.serializers.CollectionSerializer::write (183 bytes)
Event: 17264.380 Thread 0x00002ac52411a800 nmethod 5093 0x00002ac528db5dd0 code [0x00002ac528db5f40, 0x00002ac528db60e8]
Event: 17264.380 Thread 0x00002ac52411c800 nmethod 5094 0x00002ac528db6190 code [0x00002ac528db63e0, 0x00002ac528db6888]

GC Heap History (10 events):
Event: 7.864 GC heap before
{Heap before GC invocations=1 (full 0):
 PSYoungGen      total 305856K, used 262208K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 100% used [0x00000007aaab0000,0x00000007baac0000,0x00000007baac0000)
  from space 43648K, 0% used [0x00000007bd560000,0x00000007bd560000,0x00000007c0000000)
  to   space 43648K, 0% used [0x00000007baac0000,0x00000007baac0000,0x00000007bd560000)
 ParOldGen       total 699072K, used 0K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x0000000700000000,0x000000072aab0000)
 PSPermGen       total 21824K, used 21671K [0x00000006fae00000, 0x00000006fc350000, 0x0000000700000000)
  object space 21824K, 99% used [0x00000006fae00000,0x00000006fc329e28,0x00000006fc350000)
Event: 7.899 GC heap after
Heap after GC invocations=1 (full 0):
 PSYoungGen      total 305856K, used 33507K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 0% used [0x00000007aaab0000,0x00000007aaab0000,0x00000007baac0000)
  from space 43648K, 76% used [0x00000007baac0000,0x00000007bcb78fe8,0x00000007bd560000)
  to   space 43648K, 0% used [0x00000007bd560000,0x00000007bd560000,0x00000007c0000000)
 ParOldGen       total 699072K, used 40K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070000a000,0x000000072aab0000)
 PSPermGen       total 21824K, used 21671K [0x00000006fae00000, 0x00000006fc350000, 0x0000000700000000)
  object space 21824K, 99% used [0x00000006fae00000,0x00000006fc329e28,0x00000006fc350000)
}
Event: 4133.531 GC heap before
{Heap before GC invocations=2 (full 0):
 PSYoungGen      total 305856K, used 295715K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 100% used [0x00000007aaab0000,0x00000007baac0000,0x00000007baac0000)
  from space 43648K, 76% used [0x00000007baac0000,0x00000007bcb78fe8,0x00000007bd560000)
  to   space 43648K, 0% used [0x00000007bd560000,0x00000007bd560000,0x00000007c0000000)
 ParOldGen       total 699072K, used 40K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070000a000,0x000000072aab0000)
 PSPermGen       total 26048K, used 26022K [0x00000006fae00000, 0x00000006fc770000, 0x0000000700000000)
  object space 26048K, 99% used [0x00000006fae00000,0x00000006fc7699c8,0x00000006fc770000)
Event: 4133.603 GC heap after
Heap after GC invocations=2 (full 0):
 PSYoungGen      total 305856K, used 32682K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 0% used [0x00000007aaab0000,0x00000007aaab0000,0x00000007baac0000)
  from space 43648K, 74% used [0x00000007bd560000,0x00000007bf54a868,0x00000007c0000000)
  to   space 43648K, 0% used [0x00000007baac0000,0x00000007baac0000,0x00000007bd560000)
 ParOldGen       total 699072K, used 56K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070000e000,0x000000072aab0000)
 PSPermGen       total 26048K, used 26022K [0x00000006fae00000, 0x00000006fc770000, 0x0000000700000000)
  object space 26048K, 99% used [0x00000006fae00000,0x00000006fc7699c8,0x00000006fc770000)
}
Event: 6767.354 GC heap before
{Heap before GC invocations=3 (full 0):
 PSYoungGen      total 305856K, used 294890K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 100% used [0x00000007aaab0000,0x00000007baac0000,0x00000007baac0000)
  from space 43648K, 74% used [0x00000007bd560000,0x00000007bf54a868,0x00000007c0000000)
  to   space 43648K, 0% used [0x00000007baac0000,0x00000007baac0000,0x00000007bd560000)
 ParOldGen       total 699072K, used 56K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070000e000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26131K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc784f00,0x00000006fc7a0000)
Event: 6767.389 GC heap after
Heap after GC invocations=3 (full 0):
 PSYoungGen      total 305856K, used 24084K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 0% used [0x00000007aaab0000,0x00000007aaab0000,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007baac0000,0x00000007bc245140,0x00000007bd560000)
  to   space 43648K, 0% used [0x00000007bd560000,0x00000007bd560000,0x00000007c0000000)
 ParOldGen       total 699072K, used 72K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x0000000700012000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26131K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc784f00,0x00000006fc7a0000)
}
Event: 9062.867 GC heap before
{Heap before GC invocations=4 (full 0):
 PSYoungGen      total 305856K, used 286292K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 100% used [0x00000007aaab0000,0x00000007baac0000,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007baac0000,0x00000007bc245140,0x00000007bd560000)
  to   space 43648K, 0% used [0x00000007bd560000,0x00000007bd560000,0x00000007c0000000)
 ParOldGen       total 699072K, used 72K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x0000000700012000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26156K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc78b310,0x00000006fc7a0000)
Event: 9062.929 GC heap after
Heap after GC invocations=4 (full 0):
 PSYoungGen      total 305856K, used 24170K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 0% used [0x00000007aaab0000,0x00000007aaab0000,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007bd560000,0x00000007becfaa58,0x00000007c0000000)
  to   space 43648K, 0% used [0x00000007baac0000,0x00000007baac0000,0x00000007bd560000)
 ParOldGen       total 699072K, used 88K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x0000000700016000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26156K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc78b310,0x00000006fc7a0000)
}
Event: 15679.037 GC heap before
{Heap before GC invocations=5 (full 0):
 PSYoungGen      total 305856K, used 286378K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 100% used [0x00000007aaab0000,0x00000007baac0000,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007bd560000,0x00000007becfaa58,0x00000007c0000000)
  to   space 43648K, 0% used [0x00000007baac0000,0x00000007baac0000,0x00000007bd560000)
 ParOldGen       total 699072K, used 88K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x0000000700016000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26228K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc79d230,0x00000006fc7a0000)
Event: 15679.076 GC heap after
Heap after GC invocations=5 (full 0):
 PSYoungGen      total 305856K, used 24314K [0x00000007aaab0000, 0x00000007c0000000, 0x0000000800000000)
  eden space 262208K, 0% used [0x00000007aaab0000,0x00000007aaab0000,0x00000007baac0000)
  from space 43648K, 55% used [0x00000007baac0000,0x00000007bc27ea68,0x00000007bd560000)
  to   space 36416K, 0% used [0x00000007bdc70000,0x00000007bdc70000,0x00000007c0000000)
 ParOldGen       total 699072K, used 104K [0x0000000700000000, 0x000000072aab0000, 0x00000007aaab0000)
  object space 699072K, 0% used [0x0000000700000000,0x000000070001a000,0x000000072aab0000)
 PSPermGen       total 26240K, used 26228K [0x00000006fae00000, 0x00000006fc7a0000, 0x0000000700000000)
  object space 26240K, 99% used [0x00000006fae00000,0x00000006fc79d230,0x00000006fc7a0000)
}

Deoptimization events (0 events):
No events

Internal exceptions (10 events):
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07acb48 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07ad3c0 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07adc38 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07ae4b0 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07aed28 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07af5a0 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07afe18 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07b0690 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18662.659 Thread 0x00002ac524942800 Threw 0x00000007b07b0f08 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716
Event: 18820.287 Thread 0x00002ac524942800 Threw 0x00000007b084a9c0 at /HUDSON/workspace/jdk7u25-2-build-linux-amd64-product/jdk7u25/hotspot/src/share/vm/prims/jni.cpp:716

Events (10 events):
Event: 18652.684 Executing VM operation: RevokeBias done
Event: 18652.684 Thread 0x00002ac5d8013000 Thread exited: 0x00002ac5d8013000
Event: 18662.689 Executing VM operation: RevokeBias
Event: 18820.260 Thread 0x00002ac5d8013000 Thread added: 0x00002ac5d8013000
Event: 18820.272 Executing VM operation: RevokeBias done
Event: 18820.273 Executing VM operation: BulkRevokeBias
Event: 18820.275 Executing VM operation: BulkRevokeBias done
Event: 18820.276 Executing VM operation: RevokeBias
Event: 18820.276 Executing VM operation: RevokeBias done
Event: 18820.276 Thread 0x00002ac5d8013000 Thread exited: 0x00002ac5d8013000

Dynamic libraries:
00400000-00401000 r-xp 00000000 4f9:2c566 144115219499711401             /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/bin/java
00600000-00601000 rw-p 00000000 4f9:2c566 144115219499711401             /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/bin/java
012c4000-012e5000 rw-p 00000000 00:00 0                                  [heap]
6fae00000-6fc7a0000 rw-p 00000000 00:00 0 
6fc7a0000-700000000 rw-p 00000000 00:00 0 
700000000-72aab0000 rw-p 00000000 00:00 0 
72aab0000-7aaab0000 rw-p 00000000 00:00 0 
7aaab0000-7c0000000 rw-p 00000000 00:00 0 
7c0000000-800000000 rw-p 00000000 00:00 0 
2ac520359000-2ac520379000 r-xp 00000000 fd:00 425201                     /usr/lib64/ld-2.17.so
2ac520379000-2ac52037b000 r-xp 00000000 00:00 0                          [vdso]
2ac52037b000-2ac52037c000 rw-p 00000000 00:00 0 
2ac52037c000-2ac52037d000 r--p 00000000 00:00 0 
2ac52037d000-2ac52037e000 rw-p 00000000 00:00 0 
2ac52037e000-2ac520386000 rw-s 00000000 fd:02 3538987                    /tmp/hsperfdata_funk_006/14926
2ac520386000-2ac52038b000 r--s 0006d000 4f9:2c566 144116217811082510     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/io/nextflow/nxf-commons/0.24.4/nxf-commons-0.24.4.jar
2ac52038b000-2ac52038d000 r--s 0000a000 4f9:2c566 144116217811082518     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/io/nextflow/nxf-httpfs/0.24.4/nxf-httpfs-0.24.4.jar
2ac52038d000-2ac52038e000 r--s 00004000 4f9:2c566 144116217811082639     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/groovy/groovy-nio/2.4.10/groovy-nio-2.4.10.jar
2ac52038e000-2ac520391000 r--s 0001d000 4f9:2c566 144116217811082630     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/groovy/groovy-json/2.4.10/groovy-json-2.4.10.jar
2ac520391000-2ac520393000 r--s 00016000 4f9:2c566 144116217811082645     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/groovy/groovy-templates/2.4.10/groovy-templates-2.4.10.jar
2ac520393000-2ac520397000 rw-p 00000000 00:00 0 
2ac520397000-2ac52039a000 ---p 00000000 00:00 0 
2ac52039a000-2ac5204a5000 rw-p 00000000 00:00 0                          [stack:15018]
2ac5204a5000-2ac5204c1000 rw-p 00000000 00:00 0 
2ac5204c1000-2ac520559000 rw-p 00000000 00:00 0 
2ac520559000-2ac52056e000 r--s 00116000 4f9:2c566 144116217811082611     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar
2ac52056e000-2ac520570000 r--s 00003000 4f9:2c566 144116217811082722     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.21/jcl-over-slf4j-1.7.21.jar
2ac520570000-2ac520572000 r--s 00000000 4f9:2c566 144116217811082757     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/slf4j/jul-to-slf4j/1.7.21/jul-to-slf4j-1.7.21.jar
2ac520572000-2ac520574000 r--s 00004000 4f9:2c566 144116217811082762     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.21/log4j-over-slf4j-1.7.21.jar
2ac520574000-2ac520576000 r--s 00013000 4f9:2c566 144116217811082343     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/ch/grengine/grengine/1.0.3/grengine-1.0.3.jar
2ac520576000-2ac520578000 r--s 0000d000 4f9:2c566 144116217811082410     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar
2ac520578000-2ac520579000 r--s 0000e000 4f9:2c566 144116217811082676     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/jsr166-mirror/jsr166y/1.7.0/jsr166y-1.7.0.jar
2ac520579000-2ac52057a000 r--p 00020000 fd:00 425201                     /usr/lib64/ld-2.17.so
2ac52057a000-2ac52057b000 rw-p 00021000 fd:00 425201                     /usr/lib64/ld-2.17.so
2ac52057b000-2ac52057c000 rw-p 00000000 00:00 0 
2ac52057c000-2ac520593000 r-xp 00000000 fd:00 394171                     /usr/lib64/libpthread-2.17.so
2ac520593000-2ac520792000 ---p 00017000 fd:00 394171                     /usr/lib64/libpthread-2.17.so
2ac520792000-2ac520793000 r--p 00016000 fd:00 394171                     /usr/lib64/libpthread-2.17.so
2ac520793000-2ac520794000 rw-p 00017000 fd:00 394171                     /usr/lib64/libpthread-2.17.so
2ac520794000-2ac520798000 rw-p 00000000 00:00 0 
2ac520798000-2ac5207ae000 r-xp 00000000 4f9:2c566 144115219499711600     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/jli/libjli.so
2ac5207ae000-2ac5209ae000 ---p 00016000 4f9:2c566 144115219499711600     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/jli/libjli.so
2ac5209ae000-2ac5209af000 rw-p 00016000 4f9:2c566 144115219499711600     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/jli/libjli.so
2ac5209af000-2ac5209b1000 r-xp 00000000 fd:00 424783                     /usr/lib64/libdl-2.17.so
2ac5209b1000-2ac520bb1000 ---p 00002000 fd:00 424783                     /usr/lib64/libdl-2.17.so
2ac520bb1000-2ac520bb2000 r--p 00002000 fd:00 424783                     /usr/lib64/libdl-2.17.so
2ac520bb2000-2ac520bb3000 rw-p 00003000 fd:00 424783                     /usr/lib64/libdl-2.17.so
2ac520bb3000-2ac520d6a000 r-xp 00000000 fd:00 401955                     /usr/lib64/libc-2.17.so
2ac520d6a000-2ac520f69000 ---p 001b7000 fd:00 401955                     /usr/lib64/libc-2.17.so
2ac520f69000-2ac520f6d000 r--p 001b6000 fd:00 401955                     /usr/lib64/libc-2.17.so
2ac520f6d000-2ac520f6f000 rw-p 001ba000 fd:00 401955                     /usr/lib64/libc-2.17.so
2ac520f6f000-2ac520f74000 rw-p 00000000 00:00 0 
2ac520f74000-2ac5219b5000 r-xp 00000000 4f9:2c566 144115219499711602     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/server/libjvm.so
2ac5219b5000-2ac521bb5000 ---p 00a41000 4f9:2c566 144115219499711602     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/server/libjvm.so
2ac521bb5000-2ac521c58000 rw-p 00a41000 4f9:2c566 144115219499711602     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/server/libjvm.so
2ac521c58000-2ac521c94000 rw-p 00000000 00:00 0 
2ac521c94000-2ac521d94000 r-xp 00000000 fd:00 424784                     /usr/lib64/libm-2.17.so
2ac521d94000-2ac521f94000 ---p 00100000 fd:00 424784                     /usr/lib64/libm-2.17.so
2ac521f94000-2ac521f95000 r--p 00100000 fd:00 424784                     /usr/lib64/libm-2.17.so
2ac521f95000-2ac521f96000 rw-p 00101000 fd:00 424784                     /usr/lib64/libm-2.17.so
2ac521f96000-2ac521f9d000 r-xp 00000000 fd:00 424790                     /usr/lib64/librt-2.17.so
2ac521f9d000-2ac52219c000 ---p 00007000 fd:00 424790                     /usr/lib64/librt-2.17.so
2ac52219c000-2ac52219d000 r--p 00006000 fd:00 424790                     /usr/lib64/librt-2.17.so
2ac52219d000-2ac52219e000 rw-p 00007000 fd:00 424790                     /usr/lib64/librt-2.17.so
2ac52219e000-2ac5221ab000 r-xp 00000000 4f9:2c566 144115219499711597     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libverify.so
2ac5221ab000-2ac5223aa000 ---p 0000d000 4f9:2c566 144115219499711597     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libverify.so
2ac5223aa000-2ac5223ac000 rw-p 0000c000 4f9:2c566 144115219499711597     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libverify.so
2ac5223ac000-2ac5223d5000 r-xp 00000000 4f9:2c566 144115219499711567     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libjava.so
2ac5223d5000-2ac5225d5000 ---p 00029000 4f9:2c566 144115219499711567     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libjava.so
2ac5225d5000-2ac5225d7000 rw-p 00029000 4f9:2c566 144115219499711567     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libjava.so
2ac5225d7000-2ac5225e3000 r-xp 00000000 fd:00 424787                     /usr/lib64/libnss_files-2.17.so
2ac5225e3000-2ac5227e2000 ---p 0000c000 fd:00 424787                     /usr/lib64/libnss_files-2.17.so
2ac5227e2000-2ac5227e3000 r--p 0000b000 fd:00 424787                     /usr/lib64/libnss_files-2.17.so
2ac5227e3000-2ac5227e4000 rw-p 0000c000 fd:00 424787                     /usr/lib64/libnss_files-2.17.so
2ac5227e4000-2ac5227ea000 rw-p 00000000 00:00 0 
2ac5227ea000-2ac5227ed000 r-xp 00000000 fd:00 403027                     /usr/lib64/libnss_cache.so.2.0
2ac5227ed000-2ac5229ed000 ---p 00003000 fd:00 403027                     /usr/lib64/libnss_cache.so.2.0
2ac5229ed000-2ac5229ee000 rw-p 00003000 fd:00 403027                     /usr/lib64/libnss_cache.so.2.0
2ac5229ee000-2ac522a09000 r-xp 00000000 4f9:2c566 144115219499711598     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libzip.so
2ac522a09000-2ac522c08000 ---p 0001b000 4f9:2c566 144115219499711598     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libzip.so
2ac522c08000-2ac522c09000 rw-p 0001a000 4f9:2c566 144115219499711598     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libzip.so
2ac522c09000-2ac522c40000 rw-p 00000000 00:00 0 
2ac522c40000-2ac522d89000 rw-p 00000000 00:00 0 
2ac522d89000-2ac522d96000 rw-p 00000000 00:00 0 
2ac522d96000-2ac522db2000 rw-p 00000000 00:00 0 
2ac522db2000-2ac522f08000 rw-p 00000000 00:00 0 
2ac522f08000-2ac523307000 rw-p 00000000 00:00 0 
2ac523307000-2ac5233b2000 rw-p 00000000 00:00 0 
2ac5233b2000-2ac5235b2000 rw-p 00000000 00:00 0 
2ac5235b2000-2ac523709000 rw-p 00000000 00:00 0 
2ac523709000-2ac523b09000 rw-p 00000000 00:00 0 
2ac523b09000-2ac523b0a000 ---p 00000000 00:00 0 
2ac523b0a000-2ac523c0a000 rw-p 00000000 00:00 0                          [stack:15023]
2ac523c0a000-2ac523c0b000 ---p 00000000 00:00 0 
2ac523c0b000-2ac523d0b000 rw-p 00000000 00:00 0                          [stack:15024]
2ac523d0b000-2ac523d0c000 ---p 00000000 00:00 0 
2ac523d0c000-2ac523e0c000 rw-p 00000000 00:00 0                          [stack:15025]
2ac523e0c000-2ac523e0d000 ---p 00000000 00:00 0 
2ac523e0d000-2ac523ff4000 rw-p 00000000 00:00 0                          [stack:15026]
2ac523ff4000-2ac523ffb000 r--s 00045000 4f9:2c566 144116217811082348     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/ch/qos/logback/logback-classic/1.1.10/logback-classic-1.1.10.jar
2ac523ffb000-2ac524000000 r--s 00041000 4f9:2c566 144116217811082497     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar
2ac524000000-2ac524b2b000 rw-p 00000000 00:00 0 
2ac524b2b000-2ac528000000 ---p 00000000 00:00 0 
2ac528000000-2ac528dc0000 rwxp 00000000 00:00 0 
2ac528dc0000-2ac52e000000 rw-p 00000000 00:00 0 
2ac52e000000-2ac52e001000 ---p 00000000 00:00 0 
2ac52e001000-2ac52e101000 rw-p 00000000 00:00 0                          [stack:15027]
2ac52e101000-2ac52e102000 ---p 00000000 00:00 0 
2ac52e102000-2ac52e202000 rw-p 00000000 00:00 0                          [stack:15028]
2ac52e202000-2ac52e203000 ---p 00000000 00:00 0 
2ac52e203000-2ac52e303000 rw-p 00000000 00:00 0                          [stack:15029]
2ac52e303000-2ac52e304000 ---p 00000000 00:00 0 
2ac52e304000-2ac52e404000 rw-p 00000000 00:00 0                          [stack:15030]
2ac52e404000-2ac52e405000 ---p 00000000 00:00 0 
2ac52e405000-2ac52e505000 rw-p 00000000 00:00 0                          [stack:15031]
2ac52e505000-2ac52e506000 ---p 00000000 00:00 0 
2ac52e506000-2ac52e606000 rw-p 00000000 00:00 0                          [stack:15032]
2ac52e606000-2ac52e607000 ---p 00000000 00:00 0 
2ac52e607000-2ac52e707000 rw-p 00000000 00:00 0                          [stack:15033]
2ac52e707000-2ac52e708000 ---p 00000000 00:00 0 
2ac52e708000-2ac52e808000 rw-p 00000000 00:00 0                          [stack:15034]
2ac52e808000-2ac52e809000 ---p 00000000 00:00 0 
2ac52e809000-2ac52e909000 rw-p 00000000 00:00 0                          [stack:15035]
2ac52e909000-2ac52eac6000 r--s 039f9000 4f9:2c566 144115219499711545     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/rt.jar
2ac52eac6000-2ac52fffc000 rw-p 00000000 00:00 0 
2ac52fffc000-2ac52fffe000 r--s 0000a000 4f9:2c566 144116217811082527     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/io/nextflow/nxf-s3fs/1.0.0/nxf-s3fs-1.0.0.jar
2ac52fffe000-2ac530000000 r--s 00009000 4f9:2c566 144116217811082716     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar
2ac530000000-2ac530021000 rw-p 00000000 00:00 0 
2ac530021000-2ac534000000 ---p 00000000 00:00 0 
2ac534000000-2ac53767f000 rw-p 00000000 00:00 0 
2ac53767f000-2ac537680000 ---p 00000000 00:00 0 
2ac537680000-2ac537780000 rw-p 00000000 00:00 0                          [stack:15050]
2ac537780000-2ac537783000 ---p 00000000 00:00 0 
2ac537783000-2ac537881000 rw-p 00000000 00:00 0                          [stack:15060]
2ac537881000-2ac537884000 ---p 00000000 00:00 0 
2ac537884000-2ac537982000 rw-p 00000000 00:00 0                          [stack:15063]
2ac537982000-2ac537985000 ---p 00000000 00:00 0 
2ac537985000-2ac537a83000 rw-p 00000000 00:00 0                          [stack:15202]
2ac537a83000-2ac537a86000 ---p 00000000 00:00 0 
2ac537a86000-2ac537b84000 rw-p 00000000 00:00 0                          [stack:15203]
2ac537b84000-2ac537b87000 ---p 00000000 00:00 0 
2ac537b87000-2ac537c85000 rw-p 00000000 00:00 0                          [stack:15204]
2ac537c85000-2ac537c88000 ---p 00000000 00:00 0 
2ac537c88000-2ac537d86000 rw-p 00000000 00:00 0                          [stack:15207]
2ac537d86000-2ac537d89000 ---p 00000000 00:00 0 
2ac537d89000-2ac537e87000 rw-p 00000000 00:00 0                          [stack:15208]
2ac537e87000-2ac537e8a000 ---p 00000000 00:00 0 
2ac537e8a000-2ac537f88000 rw-p 00000000 00:00 0                          [stack:15209]
2ac537f88000-2ac537faa000 r--s 0016c000 4f9:2c566 144116217811082795     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/framework/0.24.4/nextflow-0.24.4-one.jar
2ac537faa000-2ac537fd2000 r--s 00369000 4f9:2c566 144116217811082502     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/io/nextflow/nextflow/0.24.4/nextflow-0.24.4.jar
2ac537fd2000-2ac537fdd000 r--s 0006a000 4f9:2c566 144116217811082358     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/ch/qos/logback/logback-core/1.1.10/logback-core-1.1.10.jar
2ac537fdd000-2ac537ff9000 r--s 00136000 4f9:2c566 144116217811082620     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar
2ac537ff9000-2ac537fff000 r--s 0004d000 4f9:2c566 144116217811082415     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
2ac537fff000-2ac538000000 r--s 0000b000 4f9:2c566 144116217811082442     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/fasterxml/jackson/dataformat/jackson-dataformat-cbor/2.6.6/jackson-dataformat-cbor-2.6.6.jar
2ac538000000-2ac538021000 rw-p 00000000 00:00 0 
2ac538021000-2ac53c000000 ---p 00000000 00:00 0 
2ac53c000000-2ac53c079000 rw-p 00000000 00:00 0 
2ac53c079000-2ac540000000 ---p 00000000 00:00 0 
2ac540000000-2ac540021000 rw-p 00000000 00:00 0 
2ac540021000-2ac544000000 ---p 00000000 00:00 0 
2ac544000000-2ac544021000 rw-p 00000000 00:00 0 
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2ac548000000-2ac548021000 rw-p 00000000 00:00 0 
2ac548021000-2ac54c000000 ---p 00000000 00:00 0 
2ac54c000000-2ac54c021000 rw-p 00000000 00:00 0 
2ac54c021000-2ac550000000 ---p 00000000 00:00 0 
2ac550000000-2ac550021000 rw-p 00000000 00:00 0 
2ac550021000-2ac554000000 ---p 00000000 00:00 0 
2ac554000000-2ac554038000 rw-p 00000000 00:00 0 
2ac554038000-2ac558000000 ---p 00000000 00:00 0 
2ac558000000-2ac558021000 rw-p 00000000 00:00 0 
2ac558021000-2ac55c000000 ---p 00000000 00:00 0 
2ac55c000000-2ac55c021000 rw-p 00000000 00:00 0 
2ac55c021000-2ac560000000 ---p 00000000 00:00 0 
2ac560000000-2ac560021000 rw-p 00000000 00:00 0 
2ac560021000-2ac564000000 ---p 00000000 00:00 0 
2ac564000000-2ac564021000 rw-p 00000000 00:00 0 
2ac564021000-2ac568000000 ---p 00000000 00:00 0 
2ac568000000-2ac568021000 rw-p 00000000 00:00 0 
2ac568021000-2ac56c000000 ---p 00000000 00:00 0 
2ac56c000000-2ac56c003000 ---p 00000000 00:00 0 
2ac56c003000-2ac56c101000 rw-p 00000000 00:00 0                          [stack:15210]
2ac56c101000-2ac56c104000 ---p 00000000 00:00 0 
2ac56c104000-2ac56c202000 rw-p 00000000 00:00 0                          [stack:15211]
2ac56c202000-2ac56c205000 ---p 00000000 00:00 0 
2ac56c205000-2ac56c303000 rw-p 00000000 00:00 0                          [stack:15212]
2ac56c303000-2ac56c306000 ---p 00000000 00:00 0 
2ac56c306000-2ac56c404000 rw-p 00000000 00:00 0                          [stack:15213]
2ac56c404000-2ac56c407000 ---p 00000000 00:00 0 
2ac56c407000-2ac56c505000 rw-p 00000000 00:00 0                          [stack:15214]
2ac56c505000-2ac56c508000 ---p 00000000 00:00 0 
2ac56c508000-2ac56c606000 rw-p 00000000 00:00 0                          [stack:15215]
2ac56c606000-2ac56c609000 ---p 00000000 00:00 0 
2ac56c609000-2ac56c707000 rw-p 00000000 00:00 0                          [stack:15216]
2ac56c707000-2ac56c70a000 ---p 00000000 00:00 0 
2ac56c70a000-2ac56c808000 rw-p 00000000 00:00 0                          [stack:15217]
2ac56c808000-2ac56c809000 ---p 00000000 00:00 0 
2ac56c809000-2ac56c909000 rw-p 00000000 00:00 0                          [stack:15220]
2ac56c909000-2ac56c956000 r--s 0040d000 4f9:2c566 144116217811082667     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/groovy/groovy/2.4.10/groovy-2.4.10.jar
2ac56c956000-2ac56c95b000 r--s 00034000 4f9:2c566 144116217811082697     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/iq80/leveldb/leveldb/0.7/leveldb-0.7.jar
2ac56c95b000-2ac56c97e000 r--s 0021b000 4f9:2c566 144116217811082684     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/4.3.1.201605051710-r/org.eclipse.jgit-4.3.1.201605051710-r.jar
2ac56c97e000-2ac56c98c000 r--s 00091000 4f9:2c566 144116217811082400     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/amazonaws/aws-java-sdk-s3/1.11.25/aws-java-sdk-s3-1.11.25.jar
2ac56c98c000-2ac56c9bc000 r--s 00344000 4f9:2c566 144116217811082380     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/amazonaws/aws-java-sdk-ec2/1.11.25/aws-java-sdk-ec2-1.11.25.jar
2ac56c9bc000-2ac56c9c4000 r--s 00078000 4f9:2c566 144116217811082543     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/javax/mail/mail/1.4.7/mail-1.4.7.jar
2ac56c9c4000-2ac56c9cb000 r--s 0003f000 4f9:2c566 144116217811082791     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/yaml/snakeyaml/1.18/snakeyaml-1.18.jar
2ac56c9cb000-2ac56c9f6000 r--s 001f5000 4f9:2c566 144116217811082468     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/google/guava/guava/16.0.1/guava-16.0.1.jar
2ac56c9f6000-2ac56c9fa000 r--s 00031000 4f9:2c566 144116217811082658     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/codehaus/groovy/groovy-xml/2.4.10/groovy-xml-2.4.10.jar
2ac56c9fa000-2ac56ca00000 r--s 00037000 4f9:2c566 144116217811082703     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar
2ac56ca00000-2ac56ca02000 r--s 00001000 4f9:2c566 144116217811082689     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/iq80/leveldb/leveldb-api/0.7/leveldb-api-0.7.jar
2ac56ca02000-2ac56ca07000 r--s 00040000 4f9:2c566 144116217811082478     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/jcraft/jsch/0.1.53/jsch-0.1.53.jar
2ac56ca07000-2ac56ca0a000 r--s 0001c000 4f9:2c566 144116217811082472     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar
2ac56ca0a000-2ac56ca11000 r--s 00058000 4f9:2c566 144116217811082388     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/amazonaws/aws-java-sdk-kms/1.11.25/aws-java-sdk-kms-1.11.25.jar
2ac56ca11000-2ac56ca22000 r--s 00097000 4f9:2c566 144116217811082372     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/amazonaws/aws-java-sdk-core/1.11.25/aws-java-sdk-core-1.11.25.jar
2ac56ca22000-2ac56ca24000 r--s 00005000 4f9:2c566 144116217811082405     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/amazonaws/jmespath-java/1.0/jmespath-java-1.0.jar
2ac56ca24000-2ac56ca26000 r--s 0000e000 4f9:2c566 144116217811082534     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/javax/activation/activation/1.1/activation-1.1.jar
2ac56ca26000-2ac56ca37000 r--s 0010d000 4f9:2c566 144116217811082437     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/fasterxml/jackson/core/jackson-databind/2.6.6/jackson-databind-2.6.6.jar
2ac56ca37000-2ac56ca47000 r--s 00088000 4f9:2c566 144116217811082550     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/joda-time/joda-time/2.8.1/joda-time-2.8.1.jar
2ac56ca47000-2ac56ca4a000 r--s 00009000 4f9:2c566 144116217811082424     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar
2ac56ca4a000-2ac56ca4e000 r--s 0003c000 4f9:2c566 144116217811082432     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/com/fasterxml/jackson/core/jackson-core/2.6.6/jackson-core-2.6.6.jar
2ac56ca4e000-2ac56ca50000 r--s 00009000 4f9:2c566 144116217811082767     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/slf4j/slf4j-api/1.7.22/slf4j-api-1.7.22.jar
2ac56ca50000-2ac56ca5d000 r--s 000a7000 4f9:2c566 144116217811082586     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/apache/httpcomponents/httpclient/4.5.2/httpclient-4.5.2.jar
2ac56ca5d000-2ac56ca64000 r--s 00049000 4f9:2c566 144116217811082603     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.jar
2ac56ca64000-2ac56ca6b000 r--s 0003a000 4f9:2c566 144116217811082490     /lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/capsule/deps/commons-codec/commons-codec/1.9/commons-codec-1.9.jar
2ac56ca6b000-2ac56ca7b000 r-xp 00000000 4f9:2c566 144115219499711586     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnio.so
2ac56ca7b000-2ac56cc7b000 ---p 00010000 4f9:2c566 144115219499711586     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnio.so
2ac56cc7b000-2ac56cc7c000 rw-p 00010000 4f9:2c566 144115219499711586     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnio.so
2ac56cc7c000-2ac56cc91000 r-xp 00000000 4f9:2c566 144115219499711585     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnet.so
2ac56cc91000-2ac56ce91000 ---p 00015000 4f9:2c566 144115219499711585     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnet.so
2ac56ce91000-2ac56ce92000 rw-p 00015000 4f9:2c566 144115219499711585     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libnet.so
2ac56ce92000-2ac56cf53000 rw-p 00000000 00:00 0 
2ac56cf53000-2ac56cf5d000 r--s 00371000 4f9:2c566 144115219499711511     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/charsets.jar
2ac56cf5d000-2ac56cf61000 r--s 000f7000 4f9:2c566 144115219499711681     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/ext/localedata.jar
2ac56cf61000-2ac56cf65000 r--s 0008a000 4f9:2c566 144115219499711535     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/jsse.jar
2ac56cf65000-2ac56cf6f000 r--s 00254000 4f9:2c566 144115219499711544     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/resources.jar
2ac56cf6f000-2ac56cf77000 r-xp 00000000 4f9:2c566 144115219499711583     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libmanagement.so
2ac56cf77000-2ac56d176000 ---p 00008000 4f9:2c566 144115219499711583     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libmanagement.so
2ac56d176000-2ac56d177000 rw-p 00007000 4f9:2c566 144115219499711583     /lupus/sw/comp/java/x86_64/sun_jdk1.7.0_25/jre/lib/amd64/libmanagement.so
2ac56d18e000-2ac56d193000 r-xp 00000000 fd:00 405194                     /usr/lib64/libnss_dns-2.17.so
2ac56d193000-2ac56d392000 ---p 00005000 fd:00 405194                     /usr/lib64/libnss_dns-2.17.so
2ac56d392000-2ac56d393000 r--p 00004000 fd:00 405194                     /usr/lib64/libnss_dns-2.17.so
2ac56d393000-2ac56d394000 rw-p 00005000 fd:00 405194                     /usr/lib64/libnss_dns-2.17.so
2ac56d394000-2ac56d3aa000 r-xp 00000000 fd:00 424789                     /usr/lib64/libresolv-2.17.so
2ac56d3aa000-2ac56d5aa000 ---p 00016000 fd:00 424789                     /usr/lib64/libresolv-2.17.so
2ac56d5aa000-2ac56d5ab000 r--p 00016000 fd:00 424789                     /usr/lib64/libresolv-2.17.so
2ac56d5ab000-2ac56d5ac000 rw-p 00017000 fd:00 424789                     /usr/lib64/libresolv-2.17.so
2ac56d5ac000-2ac56d5ae000 rw-p 00000000 00:00 0 
2ac56d5ae000-2ac56d5b1000 ---p 00000000 00:00 0 
2ac56d5b1000-2ac56d5d6000 rw-p 00000000 00:00 0 
2ac56d5d6000-2ac56d6d6000 rw-s 00000000 4f9:2c566 144116251080265003     /lupus/proj/ngi2016003/nobackup/NGI/ANALYSIS/P7709/rnaseq_ngi/.nextflow/cache/0c4296d6-8bb6-4241-add4-d77acf90612b/db/000003.log
2ac56d6d6000-2ac56d7d6000 rw-s 00000000 4f9:2c566 144116251080265004     /lupus/proj/ngi2016003/nobackup/NGI/ANALYSIS/P7709/rnaseq_ngi/.nextflow/cache/0c4296d6-8bb6-4241-add4-d77acf90612b/db/MANIFEST-000002
2ac56d7d6000-2ac56d7d9000 ---p 00000000 00:00 0 
2ac56d7d9000-2ac56d8d7000 rw-p 00000000 00:00 0 
2ac56d8d7000-2ac56d8da000 ---p 00000000 00:00 0 
2ac56d8da000-2ac56d9d8000 rw-p 00000000 00:00 0 
2ac56d9d8000-2ac56d9db000 ---p 00000000 00:00 0 
2ac56d9db000-2ac56dad9000 rw-p 00000000 00:00 0                          [stack:25151]
2ac56dad9000-2ac56dadc000 ---p 00000000 00:00 0 
2ac56dadc000-2ac56dbda000 rw-p 00000000 00:00 0                          [stack:21214]
2ac56dbda000-2ac56dbdd000 ---p 00000000 00:00 0 
2ac56dbdd000-2ac56dcdb000 rw-p 00000000 00:00 0 
2ac56dcdb000-2ac56dcde000 ---p 00000000 00:00 0 
2ac56dcde000-2ac56dddc000 rw-p 00000000 00:00 0 
2ac56dddc000-2ac56dddf000 ---p 00000000 00:00 0 
2ac56dddf000-2ac56dedd000 rw-p 00000000 00:00 0                          [stack:17160]
2ac56dedd000-2ac56dee0000 ---p 00000000 00:00 0 
2ac56dee0000-2ac56dfde000 rw-p 00000000 00:00 0 
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2ac56e1e3000-2ac56e2e1000 rw-p 00000000 00:00 0 
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2ac56e2e4000-2ac56e3e2000 rw-p 00000000 00:00 0 
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2ac56e3e5000-2ac56e4e3000 rw-p 00000000 00:00 0 
2ac56e4e3000-2ac56e4e6000 ---p 00000000 00:00 0 
2ac56e4e6000-2ac56e5e4000 rw-p 00000000 00:00 0 
2ac56e5e4000-2ac56e5e7000 ---p 00000000 00:00 0 
2ac56e5e7000-2ac56e6e5000 rw-p 00000000 00:00 0 
2ac56e6e5000-2ac56e6e8000 ---p 00000000 00:00 0 
2ac56e6e8000-2ac56e7e6000 rw-p 00000000 00:00 0 
2ac56e7e6000-2ac56e7e9000 ---p 00000000 00:00 0 
2ac56e7e9000-2ac56e8e7000 rw-p 00000000 00:00 0 
2ac56e8e7000-2ac56e8ea000 ---p 00000000 00:00 0 
2ac56e8ea000-2ac56e9e8000 rw-p 00000000 00:00 0 
2ac56e9e8000-2ac56e9eb000 ---p 00000000 00:00 0 
2ac56e9eb000-2ac56eae9000 rw-p 00000000 00:00 0 
2ac56eae9000-2ac56eaec000 ---p 00000000 00:00 0 
2ac56eaec000-2ac56ebea000 rw-p 00000000 00:00 0                          [stack:12717]
2ac56ebea000-2ac56ebed000 ---p 00000000 00:00 0 
2ac56ebed000-2ac56eceb000 rw-p 00000000 00:00 0 
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2ac56eef0000-2ac56efee000 rw-p 00000000 00:00 0 
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2ac56eff1000-2ac56f0ef000 rw-p 00000000 00:00 0 
2ac56f0ef000-2ac56f0f2000 ---p 00000000 00:00 0 
2ac56f0f2000-2ac56f1f0000 rw-p 00000000 00:00 0 
2ac56f1f0000-2ac56f1f3000 ---p 00000000 00:00 0 
2ac56f1f3000-2ac56f2f1000 rw-p 00000000 00:00 0 
2ac56f2f1000-2ac56f2f4000 ---p 00000000 00:00 0 
2ac56f2f4000-2ac56f3f2000 rw-p 00000000 00:00 0 
2ac56f3f2000-2ac56f3f5000 ---p 00000000 00:00 0 
2ac56f3f5000-2ac56f4f3000 rw-p 00000000 00:00 0 
2ac56f4f3000-2ac56f4f6000 ---p 00000000 00:00 0 
2ac56f4f6000-2ac56f5f4000 rw-p 00000000 00:00 0 
2ac56f5f4000-2ac56f5f7000 ---p 00000000 00:00 0 
2ac56f5f7000-2ac56f6f5000 rw-p 00000000 00:00 0 
2ac56f6f5000-2ac56f6f8000 ---p 00000000 00:00 0 
2ac56f6f8000-2ac56f7f6000 rw-p 00000000 00:00 0                          [stack:21697]
2ac56f7f6000-2ac56f7f9000 ---p 00000000 00:00 0 
2ac56f7f9000-2ac56f81e000 rw-p 00000000 00:00 0                          [stack:13384]
2ac570000000-2ac570021000 rw-p 00000000 00:00 0 
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2ac588000000-2ac58e529000 r--p 00000000 fd:00 668473                     /usr/lib/locale/locale-archive
2ac590000000-2ac590021000 rw-p 00000000 00:00 0 
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2ac59c000000-2ac59c021000 rw-p 00000000 00:00 0 
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2ac5a0000000-2ac5a0021000 rw-p 00000000 00:00 0 
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2ac5ac3d9000-2ac5b0000000 ---p 00000000 00:00 0 
2ac5b0000000-2ac5b01f7000 rw-p 00000000 00:00 0 
2ac5b01f7000-2ac5b4000000 ---p 00000000 00:00 0 
2ac5b4000000-2ac5b424f000 rw-p 00000000 00:00 0 
2ac5b424f000-2ac5b8000000 ---p 00000000 00:00 0 
2ac5b8000000-2ac5b83d8000 rw-p 00000000 00:00 0 
2ac5b83d8000-2ac5bc000000 ---p 00000000 00:00 0 
2ac5bc000000-2ac5bc021000 rw-p 00000000 00:00 0 
2ac5bc021000-2ac5c0000000 ---p 00000000 00:00 0 
2ac5c0000000-2ac5c0021000 rw-p 00000000 00:00 0 
2ac5c0021000-2ac5c4000000 ---p 00000000 00:00 0 
2ac5c4000000-2ac5c4021000 rw-p 00000000 00:00 0 
2ac5c4021000-2ac5c8000000 ---p 00000000 00:00 0 
2ac5c8000000-2ac5c8021000 rw-p 00000000 00:00 0 
2ac5c8021000-2ac5cc000000 ---p 00000000 00:00 0 
2ac5cc000000-2ac5cc021000 rw-p 00000000 00:00 0 
2ac5cc021000-2ac5d0000000 ---p 00000000 00:00 0 
2ac5d0000000-2ac5d0021000 rw-p 00000000 00:00 0 
2ac5d0021000-2ac5d4000000 ---p 00000000 00:00 0 
2ac5d4000000-2ac5d4021000 rw-p 00000000 00:00 0 
2ac5d4021000-2ac5d8000000 ---p 00000000 00:00 0 
2ac5d8000000-2ac5d8033000 rw-p 00000000 00:00 0 
2ac5d8033000-2ac5dc000000 ---p 00000000 00:00 0 
2ac5dc000000-2ac5dc04c000 rw-p 00000000 00:00 0 
2ac5dc04c000-2ac5e0000000 ---p 00000000 00:00 0 
2ac5e0000000-2ac5e0021000 rw-p 00000000 00:00 0 
2ac5e0021000-2ac5e4000000 ---p 00000000 00:00 0 
2ac5e4000000-2ac5e4021000 rw-p 00000000 00:00 0 
2ac5e4021000-2ac5e8000000 ---p 00000000 00:00 0 
2ac5e8000000-2ac5e8021000 rw-p 00000000 00:00 0 
2ac5e8021000-2ac5ec000000 ---p 00000000 00:00 0 
2ac5ec000000-2ac5ec021000 rw-p 00000000 00:00 0 
2ac5ec021000-2ac5f0000000 ---p 00000000 00:00 0 
2ac5f0000000-2ac5f0021000 rw-p 00000000 00:00 0 
2ac5f0021000-2ac5f4000000 ---p 00000000 00:00 0 
2ac5f4000000-2ac5f4021000 rw-p 00000000 00:00 0 
2ac5f4021000-2ac5f8000000 ---p 00000000 00:00 0 
2ac5f8000000-2ac5f8021000 rw-p 00000000 00:00 0 
2ac5f8021000-2ac5fc000000 ---p 00000000 00:00 0 
2ac5fc000000-2ac5fc021000 rw-p 00000000 00:00 0 
2ac5fc021000-2ac600000000 ---p 00000000 00:00 0 
2ac600000000-2ac600021000 rw-p 00000000 00:00 0 
2ac600021000-2ac604000000 ---p 00000000 00:00 0 
2ac604000000-2ac604021000 rw-p 00000000 00:00 0 
2ac604021000-2ac608000000 ---p 00000000 00:00 0 
2ac608000000-2ac608021000 rw-p 00000000 00:00 0 
2ac608021000-2ac60c000000 ---p 00000000 00:00 0 
2ac60c000000-2ac60c029000 rw-p 00000000 00:00 0 
2ac60c029000-2ac610000000 ---p 00000000 00:00 0 
2ac610000000-2ac610021000 rw-p 00000000 00:00 0 
2ac610021000-2ac614000000 ---p 00000000 00:00 0 
2ac614000000-2ac61402a000 rw-p 00000000 00:00 0 
2ac61402a000-2ac618000000 ---p 00000000 00:00 0 
2ac618000000-2ac618021000 rw-p 00000000 00:00 0 
2ac618021000-2ac61c000000 ---p 00000000 00:00 0 
2ac61c000000-2ac61c021000 rw-p 00000000 00:00 0 
2ac61c021000-2ac620000000 ---p 00000000 00:00 0 
2ac620000000-2ac620021000 rw-p 00000000 00:00 0 
2ac620021000-2ac624000000 ---p 00000000 00:00 0 
2ac624000000-2ac624021000 rw-p 00000000 00:00 0 
2ac624021000-2ac628000000 ---p 00000000 00:00 0 
2ac628000000-2ac628021000 rw-p 00000000 00:00 0 
2ac628021000-2ac62c000000 ---p 00000000 00:00 0 
2ac62c000000-2ac62c021000 rw-p 00000000 00:00 0 
2ac62c021000-2ac630000000 ---p 00000000 00:00 0 
2ac630000000-2ac630021000 rw-p 00000000 00:00 0 
2ac630021000-2ac634000000 ---p 00000000 00:00 0 
2ac634000000-2ac634021000 rw-p 00000000 00:00 0 
2ac634021000-2ac638000000 ---p 00000000 00:00 0 
2ac638000000-2ac638021000 rw-p 00000000 00:00 0 
2ac638021000-2ac63c000000 ---p 00000000 00:00 0 
2ac63c000000-2ac63c021000 rw-p 00000000 00:00 0 
2ac63c021000-2ac640000000 ---p 00000000 00:00 0 
2ac640000000-2ac640033000 rw-p 00000000 00:00 0 
2ac640033000-2ac644000000 ---p 00000000 00:00 0 
2ac644000000-2ac644021000 rw-p 00000000 00:00 0 
2ac644021000-2ac648000000 ---p 00000000 00:00 0 
2ac648000000-2ac648021000 rw-p 00000000 00:00 0 
2ac648021000-2ac64c000000 ---p 00000000 00:00 0 
7fff48608000-7fff4872d000 rw-p 00000000 00:00 0                          [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Xverify:none -XX:+TieredCompilation -XX:TieredStopAtLevel=1 -Xms1g -Xmx4g -Djava.io.tmpdir=/proj/ngi2016003/nobackup/NGI/ANALYSIS/P7709/rnaseq_ngi/work -Dcapsule.app=nextflow_0.24.4 -Djava.awt.headless=true -Djava.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib -Dcapsule.jar=/lupus/ngi/production/v1.8.2/sw/nextflow/workfiles/framework/0.24.4/nextflow-0.24.4-one.jar -Dfile.encoding=UTF-8 
java_command: nextflow.cli.Launcher /lupus/ngi/production/v1.8.2/sw//ngi-rnaseq/main.nf -c /lupus/ngi/production/v1.8.2/conf//ngi-rnaseq_sthlm.config --reads P7709*{R1,R2}.fastq.gz --genome GRCh37 --unstranded
Launcher Type: SUN_STANDARD

Environment Variables:
JAVA_HOME=/sw/comp/java/x86_64/sun_jdk1.7.0_25
PATH=/lupus/ngi/production/v1.8.2/sw/anaconda/envs/NGI/bin:/lupus/ngi/production/v1.8.2/sw//KmerGenie/:/lupus/ngi/production/v1.8.2/sw/nextflow:/lupus/ngi/production/v1.8.2/sw//anaconda/bin:/sw/apps/bioinfo/piper/1.5.1/irma/setupfilecreator/bin:/sw/apps/bioinfo/piper/1.5.1/irma/piper/workflows:/sw/apps/bioinfo/piper/1.5.1/irma/piper/bin:/sw/comp/java/x86_64/sun_jdk1.7.0_25/bin:/usr/local/mover/1.0.0:/lupus/ngi/production/v1.8.2/sw/KmerGenie:/lupus/ngi/production/v1.8.2/sw/nextflow:/lupus/ngi/production/v1.8.2/sw/anaconda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/lupus/ngi/production/v1.8.2/sw/standalone_scripts:/home/funk_006/.local/bin:/home/funk_006/bin:/sw/uppmax/bin:/lupus/ngi/production/v1.8.2/sw//standalone_scripts
SHELL=/bin/bash

Signal Handlers:

[error occurred during error reporting (printing signal handlers), id 0x7]

---------------  S Y S T E M  ---------------

OS:CentOS Linux release 7.3.1611 (Core) 

uname:Linux 3.10.0-514.21.2.el7.x86_64 #1 SMP Tue Jun 20 12:24:47 UTC 2017 x86_64
libc:glibc 2.17 NPTL 2.17 
rlimit: STACK infinity, CORE 10k, NPROC 4096, NOFILE 16384, AS infinity
load average:21.08 17.69 11.21

/proc/meminfo:
MemTotal:       263868000 kB
MemFree:         5265176 kB
MemAvailable:   243899620 kB
Buffers:           50220 kB
Cached:         241406152 kB
SwapCached:        41748 kB
Active:         66236176 kB
Inactive:       176409164 kB
Active(anon):    1077460 kB
Inactive(anon):  1313140 kB
Active(file):   65158716 kB
Inactive(file): 175096024 kB
Unevictable:           0 kB
Mlocked:               0 kB
SwapTotal:       8388604 kB
SwapFree:        7490004 kB
Dirty:               348 kB
Writeback:      42277596 kB
AnonPages:       1147860 kB
Mapped:            46848 kB
Shmem:           1201348 kB
Slab:           14213012 kB
SReclaimable:    5194756 kB
SUnreclaim:      9018256 kB
KernelStack:        9840 kB
PageTables:        19452 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    140322604 kB
Committed_AS:    5506760 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      716016 kB
VmallocChunk:   34222632956 kB
HardwareCorrupted:     0 kB
AnonHugePages:      2048 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:      546228 kB
DirectMap2M:    15073280 kB
DirectMap1G:    254803968 kB

CPU:total 16 (8 cores per cpu, 2 threads per core) family 6 model 63 stepping 2, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, ht, tsc, tscinvbit

/proc/cpuinfo:
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1696.687
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 0
cpu cores   : 8
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 1
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1474.031
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 1
cpu cores   : 8
apicid      : 2
initial apicid  : 2
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 2
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1453.125
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 2
cpu cores   : 8
apicid      : 4
initial apicid  : 4
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 3
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1563.281
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 3
cpu cores   : 8
apicid      : 6
initial apicid  : 6
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 4
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1515.937
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 4
cpu cores   : 8
apicid      : 8
initial apicid  : 8
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 5
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1587.187
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 5
cpu cores   : 8
apicid      : 10
initial apicid  : 10
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 6
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1597.500
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 6
cpu cores   : 8
apicid      : 12
initial apicid  : 12
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1588.312
cache size  : 20480 KB
physical id : 0
siblings    : 8
core id     : 7
cpu cores   : 8
apicid      : 14
initial apicid  : 14
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4800.01
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 8
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2198.718
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 0
cpu cores   : 8
apicid      : 16
initial apicid  : 16
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 9
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2198.812
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 1
cpu cores   : 8
apicid      : 18
initial apicid  : 18
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 10
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2399.906
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 2
cpu cores   : 8
apicid      : 20
initial apicid  : 20
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 11
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2196.093
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 3
cpu cores   : 8
apicid      : 22
initial apicid  : 22
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 12
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 1998.750
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 4
cpu cores   : 8
apicid      : 24
initial apicid  : 24
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 13
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2100.562
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 5
cpu cores   : 8
apicid      : 26
initial apicid  : 26
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 14
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2195.531
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 6
cpu cores   : 8
apicid      : 28
initial apicid  : 28
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 15
vendor_id   : GenuineIntel
cpu family  : 6
model       : 63
model name  : Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
stepping    : 2
microcode   : 0x38
cpu MHz     : 2400.000
cache size  : 20480 KB
physical id : 1
siblings    : 8
core id     : 7
cpu cores   : 8
apicid      : 30
initial apicid  : 30
fpu     : yes
fpu_exception   : yes
cpuid level : 15
wp      : yes
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 arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer xsave avx f16c rdrand lahf_lm abm ida arat epb pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc
bogomips    : 4804.81
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

Memory: 4k page, physical 263868000k(5266064k free), swap 8388604k(7490004k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (23.25-b01) for linux-amd64 JRE (1.7.0_25-b15), built on Jun  5 2013 20:48:36 by "java_re" with gcc 4.3.0 20080428 (Red Hat 4.3.0-8)

time: Tue Jul 11 20:17:35 2017
elapsed time: 18820 seconds
pditommaso commented 7 years ago

How many times happened this crash?

sylvinite commented 7 years ago

Just once, haven't been able to reproduce it yet.

pditommaso commented 7 years ago

Very hard to say. Look at the stack trace it looks a low level JVM or operating system bug. 

j  java.lang.ClassLoader$NativeLibrary.find(Ljava/lang/String;)J+0
j  java.lang.ClassLoader.findNative(Ljava/lang/ClassLoader;Ljava/lang/String;)J+49
v  ~StubRoutines::call_stub
j  sun.nio.fs.UnixNativeDispatcher.strerror(I)[B+0
J  sun.nio.fs.UnixException.translateToIOException(Ljava/lang/String;Ljava/lang/String;)Ljava/io/IOException;
J  sun.nio.fs.UnixException.rethrowAsIOException(Lsun/nio/fs/UnixPath;Lsun/nio/fs/UnixPath;)V
J  sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes()Ljava/nio/file/attribute/BasicFileAttributes;
J  sun.nio.fs.UnixFileSystemProvider.readAttributes(Ljava/nio/file/Path;Ljava/lang/Class;[Ljava/nio/file/LinkOption;)Ljava/nio/file/attribute/BasicFileAttributes;

In any case I would try to update to the latest version of Java.

sylvinite commented 7 years ago

Okay, I'll keep that in mind :) I will close this issue and re-open it if we're able to reproduce the issue without solving .