#7 sh: line 1: 97820 Abort trap: 6

[Anonymous]

Originally created by: tomo... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. Trying to assemble Illumina read pairs (900 000 pairs)

What is the expected output? What do you see instead?
This is what I see:
Message: start iteration from mink = 29 to maxk = 90
Message: k = 29, remove 1016 dead end, 4 stand alone, remain 1009 branches
Message: k = 30, remove 220 dead end, 1 stand alone, remain 795 branches
Message: k = 31, remove 90 dead end, 2 stand alone, remain 710 branches
Message: k = 32, remove 37 dead end, 3 stand alone, remain 682 branches
Message: k = 33, remove 17 dead end, 0 stand alone, remain 648 branches
Message: k = 34, remove 4 dead end, 0 stand alone, remain 663 branches
Message: k = 35, remove 6 dead end, 0 stand alone, remain 647 branches
Message: k = 36, remove 5 dead end, 0 stand alone, remain 646 branches
Message: k = 37, remove 7 dead end, 0 stand alone, remain 642 branches
Message: k = 38, remove 5 dead end, 0 stand alone, remain 639 branches
Message: k = 39, remove 3 dead end, 0 stand alone, remain 625 branches
Message: k = 40, remove 1 dead end, 0 stand alone, remain 628 branches
sh: line 1: 97820 Abort trap: 6           /Users/tomk/ngopt_a5pipeline_macOS-x64_20130326/bin/idba -r VTgenome_A5_100.s2/VTgenome_A5_100.ec.fasta -o VTgenome_A5_100.s2/VTgenome_A5_100 --mink 29 --maxk 90 > VTgenome_A5_100.s2/idba.out
[a5] Error building contigs with IDBA

What version of the product are you using? On what operating system?
ngopt_a5pipeline_macOS-x64_20130326.
OS X 10.7.5, IMac, 8 G memory

Please provide any additional information below.
Originally tried with 250 bp reads, trimmed the reads to 150, then to 100 nt. The above is the end of the output from the 100 nt library. The other runs ended in similar ways, all with Abort trap 6
Also tried the 250 bp library on a Macbook Pro with 8 G memory, OS X 10.8.3. Last lines of output:
[a5_s2] Building contigs from VT1genome.ec.fastq with IDBA
[a5_s2] Building contigs from VT1genome.ec.fastq with IDBA
[a5] idba -r VT1genome.s2/VT1genome.ec.fasta -o VT1genome.s2/VT1genome --mink 29 --maxk 90
idba(746) malloc: *** error for object 0x1003055b8: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
sh: line 1:   746 Abort trap: 6           /Users/tomk/ngopt_a5pipeline_macOS-x64_20130326/bin/idba -r VT1genome.s2/VT1genome.ec.fasta -o VT1genome.s2/VT1genome --mink 29 --maxk 90 > VT1genome.s2/idba.out
[a5] Error building contigs with IDBA

[Anonymous]

Originally posted by: karsten.... (code.google.com)@gmail.com

I second that. A5 used to run fine, however, this particular data set (although run on the same machine as all the others before) results in the mentioned error on an MBP and an iMac both running 10.8.4 (though  - as I said - other data sets ran just fine on these machines).

Any tweaks to get idba running? It seems that it actually crashed. Here's the crash log:

Process:         idba [2423]
Path:            /Applications/Apps/*/idba
Identifier:      idba
Version:         ???
Code Type:       X86-64 (Native)
Parent Process:  sh [2422]
User ID:         501

Date/Time:       2013-07-02 01:48:57.571 +0200
OS Version:      Mac OS X 10.8.4 (12E55)
Report Version:  10

Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Exception Type:  EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000

Application Specific Information:
*** error for object 0x100305eb8: incorrect checksum for freed object - object was probably modified after being freed.

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib            0x00007fff8e8a6d46 __kill + 10
1   libsystem_c.dylib                 0x00007fff83895df0 abort + 177
2   libsystem_c.dylib                 0x00007fff83871905 szone_error + 580
3   libsystem_c.dylib                 0x00007fff8387620a tiny_malloc_from_free_list + 146
4   libsystem_c.dylib                 0x00007fff83876b38 szone_malloc_should_clear + 971
5   libsystem_c.dylib                 0x00007fff838691b3 malloc_zone_malloc + 71
6   libsystem_c.dylib                 0x00007fff83869c07 malloc + 41
7   libstdc++.6.dylib                 0x00007fff83bc2347 operator new(unsigned long) + 34
8   libstdc++.6.dylib                 0x00007fff83baf43e std::string::_Rep::_S_create(unsigned long, unsigned long, std::allocator<char> const&) + 104
9   libstdc++.6.dylib                 0x00007fff83baf38b std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned long) + 35
10  libstdc++.6.dylib                 0x00007fff83bafe56 std::string::reserve(unsigned long) + 62
11  libstdc++.6.dylib                 0x00007fff83bb01a7 std::string::append(char const*, unsigned long) + 101
12  libstdc++.6.dylib                 0x00007fff83b9a2de std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) + 237
13  idba                              0x000000010000ef38 std::vector<std::string, std::allocator<std::string> >::_M_fill_insert(__gnu_cxx::__normal_iterator<std::string*, std::vector<std::string, std::allocator<std::string> > >, unsigned long, std::string const&) + 5512
14  idba                              0x000000010001231d std::vector<OptionSet::Option, std::allocator<OptionSet::Option> >::_M_insert_aux(__gnu_cxx::__normal_iterator<OptionSet::Option*, std::vector<OptionSet::Option, std::allocator<OptionSet::Option> > >, OptionSet::Option const&) + 2909
15  idba                              0x000000010001230a std::vector<OptionSet::Option, std::allocator<OptionSet::Option> >::_M_insert_aux(__gnu_cxx::__normal_iterator<OptionSet::Option*, std::vector<OptionSet::Option, std::allocator<OptionSet::Option> > >, OptionSet::Option const&) + 2890
16  idba                              0x0000000100012398 std::vector<OptionSet::Option, std::allocator<OptionSet::Option> >::_M_insert_aux(__gnu_cxx::__normal_iterator<OptionSet::Option*, std::vector<OptionSet::Option, std::allocator<OptionSet::Option> > >, OptionSet::Option const&) + 3032
17  idba                              0x0000000100012438 std::vector<OptionSet::Option, std::allocator<OptionSet::Option> >::_M_insert_aux(__gnu_cxx::__normal_iterator<OptionSet::Option*, std::vector<OptionSet::Option, std::allocator<OptionSet::Option> > >, OptionSet::Option const&) + 3192
18  idba                              0x0000000100013141 std::vector<OptionSet::Option, std::allocator<OptionSet::Option> >::_M_insert_aux(__gnu_cxx::__normal_iterator<OptionSet::Option*, std::vector<OptionSet::Option, std::allocator<OptionSet::Option> > >, OptionSet::Option const&) + 6529
19  idba                              0x0000000100018c78 std::deque<Sequence, std::allocator<Sequence> >::_M_fill_insert(std::_Deque_iterator<Sequence, Sequence&, Sequence*>, unsigned long, Sequence const&) + 10344
20  idba                              0x0000000100019e9a std::deque<Sequence, std::allocator<Sequence> >::_M_fill_insert(std::_Deque_iterator<Sequence, Sequence&, Sequence*>, unsigned long, Sequence const&) + 14986
21  idba                              0x0000000100005276 std::_Deque_base<Read, std::allocator<Read> >::~_Deque_base() + 14198
22  idba                              0x0000000100002828 std::_Deque_base<Read, std::allocator<Read> >::~_Deque_base() + 3368

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x00007fff5fbfec20  rcx: 0x00007fff5fbfec08  rdx: 0x0000000000000000
  rdi: 0x0000000000000977  rsi: 0x0000000000000006  rbp: 0x00007fff5fbfec30  rsp: 0x00007fff5fbfec08
   [r8]: 0x00007fff5fbffb18   [r9]: 0x00000000fffffff0  [r10]: 0x00007fff8e8a8342  [r11]: 0x0000000000000206
  [r12]: 0x0000000100290000  [r13]: 0x0000000100305eb8  [r14]: 0x00000001002c20c0  [r15]: 0x0000000000000000
  rip: 0x00007fff8e8a6d46  rfl: 0x0000000000000206  cr2: 0x00007fff73437ff0
Logical CPU: 0

Binary Images:
       0x100000000 -        0x100072ff7 +idba (???) <73092F42-8988-1CAA-4EE8-55869C8F112F> /Applications/Apps/*/idba
    0x7fff651fa000 -     0x7fff6522e93f  dyld (210.2.3) <A40597AA-5529-3337-8C09-D8A014EB1578> /usr/lib/dyld
    0x7fff8383c000 -     0x7fff83908ff7  libsystem_c.dylib (825.26) <4C9EB006-FE1F-3F8F-8074-DFD94CF2CE7B> /usr/lib/system/libsystem_c.dylib
    0x7fff83a0c000 -     0x7fff83a21ff7  libdispatch.dylib (228.23) <D26996BF-FC57-39EB-8829-F63585561E09> /usr/lib/system/libdispatch.dylib
    0x7fff83a22000 -     0x7fff83a2aff7  libsystem_dnssd.dylib (379.38.1) <BDCB8566-0189-34C0-9634-35ABD3EFE25B> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff83ad8000 -     0x7fff83ad9ff7  libremovefile.dylib (23.2) <6763BC8E-18B8-3AD9-8FFA-B43713A7264F> /usr/lib/system/libremovefile.dylib
    0x7fff83b81000 -     0x7fff83beafff  libstdc++.6.dylib (56) <EAA2B53E-EADE-39CF-A0EF-FB9D4940672A> /usr/lib/libstdc++.6.dylib
    0x7fff840c3000 -     0x7fff840d1ff7  libsystem_network.dylib (77.10) <0D99F24E-56FE-380F-B81B-4A4C630EE587> /usr/lib/system/libsystem_network.dylib
    0x7fff840d2000 -     0x7fff841ea92f  libobjc.A.dylib (532.2) <90D31928-F48D-3E37-874F-220A51FD9E37> /usr/lib/libobjc.A.dylib
    0x7fff84566000 -     0x7fff845b2ff7  libauto.dylib (185.4) <AD5A4CE7-CB53-313C-9FAE-673303CC2D35> /usr/lib/libauto.dylib
    0x7fff847b2000 -     0x7fff8481aff7  libc++.1.dylib (65.1) <20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib
    0x7fff8481b000 -     0x7fff84820fff  libcompiler_rt.dylib (30) <08F8731D-5961-39F1-AD00-4590321D24A9> /usr/lib/system/libcompiler_rt.dylib
    0x7fff849d9000 -     0x7fff849dbfff  libquarantine.dylib (52.1) <143B726E-DF47-37A8-90AA-F059CFD1A2E4> /usr/lib/system/libquarantine.dylib
    0x7fff85421000 -     0x7fff85443ff7  libxpc.dylib (140.43) <70BC645B-6952-3264-930C-C835010CCEF9> /usr/lib/system/libxpc.dylib
    0x7fff85569000 -     0x7fff85577fff  libcommonCrypto.dylib (60027) <BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib
    0x7fff868c5000 -     0x7fff868cbfff  libmacho.dylib (829) <BF332AD9-E89F-387E-92A4-6E1AB74BD4D9> /usr/lib/system/libmacho.dylib
    0x7fff86987000 -     0x7fff869bdfff  libsystem_info.dylib (406.17) <4FFCA242-7F04-365F-87A6-D4EFB89503C1> /usr/lib/system/libsystem_info.dylib
    0x7fff86aef000 -     0x7fff86b1dff7  libsystem_m.dylib (3022.6) <B434BE5C-25AB-3EBD-BAA7-5304B34E3441> /usr/lib/system/libsystem_m.dylib
    0x7fff86f52000 -     0x7fff86f57fff  libcache.dylib (57) <65187C6E-3FBF-3EB8-A1AA-389445E2984D> /usr/lib/system/libcache.dylib
    0x7fff879c5000 -     0x7fff879cdfff  liblaunch.dylib (442.26.2) <2F71CAF8-6524-329E-AC56-C506658B4C0C> /usr/lib/system/liblaunch.dylib
    0x7fff879ce000 -     0x7fff87a1dff7  libcorecrypto.dylib (106.2) <CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib
    0x7fff87bfa000 -     0x7fff87c1fff7  libc++abi.dylib (26) <D86169F3-9F31-377A-9AF3-DB17142052E4> /usr/lib/libc++abi.dylib
    0x7fff8811e000 -     0x7fff88120ff7  libunc.dylib (25) <92805328-CD36-34FF-9436-571AB0485072> /usr/lib/system/libunc.dylib
    0x7fff88121000 -     0x7fff88121fff  libkeymgr.dylib (25) <CC9E3394-BE16-397F-926B-E579B60EE429> /usr/lib/system/libkeymgr.dylib
    0x7fff89a0b000 -     0x7fff89a0cff7  libsystem_sandbox.dylib (220.3) <B739DA63-B675-387A-AD84-412A651143C0> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff8b086000 -     0x7fff8b08cff7  libunwind.dylib (35.1) <21703D36-2DAB-3D8B-8442-EAAB23C060D3> /usr/lib/system/libunwind.dylib
    0x7fff8db31000 -     0x7fff8db38fff  libcopyfile.dylib (89) <876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib
    0x7fff8df12000 -     0x7fff8df13ff7  libdnsinfo.dylib (453.19) <14202FFB-C3CA-3FCC-94B0-14611BF8692D> /usr/lib/system/libdnsinfo.dylib
    0x7fff8e61e000 -     0x7fff8e61ffff  libsystem_blocks.dylib (59) <D92DCBC3-541C-37BD-AADE-ACC75A0C59C8> /usr/lib/system/libsystem_blocks.dylib
    0x7fff8e702000 -     0x7fff8e70dfff  libsystem_notify.dylib (98.5) <C49275CC-835A-3207-AFBA-8C01374927B6> /usr/lib/system/libsystem_notify.dylib
    0x7fff8e895000 -     0x7fff8e8b0ff7  libsystem_kernel.dylib (2050.24.15) <A9F97289-7985-31D6-AF89-151830684461> /usr/lib/system/libsystem_kernel.dylib
    0x7fff8e8b1000 -     0x7fff8e8b2ff7  libSystem.B.dylib (169.3) <365477AB-D641-389D-B8F4-A1FAE9657EEE> /usr/lib/libSystem.B.dylib
    0x7fff8e95c000 -     0x7fff8e95fff7  libdyld.dylib (210.2.3) <F59367C9-C110-382B-A695-9035A6DD387E> /usr/lib/system/libdyld.dylib
    0x7fff90247000 -     0x7fff90248fff  libDiagnosticMessagesClient.dylib (8) <8548E0DC-0D2F-30B6-B045-FE8A038E76D8> /usr/lib/libDiagnosticMessagesClient.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 12463
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=57.5M resident=27.2M(47%) swapped_out_or_unallocated=30.3M(53%)
Writable regions: Total=91.1M written=71.8M(79%) resident=71.8M(79%) swapped_out=0K(0%) unallocated=19.2M(21%)

REGION TYPE                      VIRTUAL
===========                      =======
MALLOC                             80.8M
MALLOC guard page                    16K
STACK GUARD                        56.0M
Stack                              8192K
VM_ALLOCATE                           4K
__DATA                             2732K
__LINKEDIT                         52.2M
__TEXT                             5456K
shared memory                        12K
===========                      =======
TOTAL                             205.0M

THX for looking into it,

Karsten

[Anonymous]

Originally posted by: karsten.... (code.google.com)@gmail.com

OK, I tried it on a Linux machine (latest Ubintu) and got this IDBA crash:

[a5_s2] Building contigs from myceto.ec.fastq with IDBA
[a5_s2] Building contigs from myceto.ec.fastq with IDBA
[a5] idba -r myceto.s2/myceto.ec.fasta -o myceto.s2/myceto --mink 29 --maxk 90
*** Error in `/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba': double free or corruption (out): 0x00000000019a4590 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x80a46)[0x7f1d02a82a46]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45c3a1]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45c777]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45fd16]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45bb18]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x4159c6]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x416b42]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x405d89]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f1d02a23ea5]
/home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba(__gxx_personality_v0+0x111)[0x4032d9]
======= Memory map: ========
00400000-0046f000 r-xp 00000000 08:06 791246                             /home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba
0066f000-00670000 rw-p 0006f000 08:06 791246                             /home/karsten/Desktop/ngopt_a5pipeline_linux-x64_20130326/bin/idba
00670000-00870000 rw-p 00000000 00:00 0
0199e000-019bf000 rw-p 00000000 00:00 0                                  [heap]
7f1d01e5f000-7f1d02a02000 rw-p 00000000 00:00 0
7f1d02a02000-7f1d02bc0000 r-xp 00000000 08:06 1840057                    /lib/x86_64-linux-gnu/libc-2.17.so
7f1d02bc0000-7f1d02dbf000 ---p 001be000 08:06 1840057                    /lib/x86_64-linux-gnu/libc-2.17.so
7f1d02dbf000-7f1d02dc3000 r--p 001bd000 08:06 1840057                    /lib/x86_64-linux-gnu/libc-2.17.so
7f1d02dc3000-7f1d02dc5000 rw-p 001c1000 08:06 1840057                    /lib/x86_64-linux-gnu/libc-2.17.so
7f1d02dc5000-7f1d02dca000 rw-p 00000000 00:00 0
7f1d02dca000-7f1d02de2000 r-xp 00000000 08:06 1840062                    /lib/x86_64-linux-gnu/libpthread-2.17.so
7f1d02de2000-7f1d02fe1000 ---p 00018000 08:06 1840062                    /lib/x86_64-linux-gnu/libpthread-2.17.so
7f1d02fe1000-7f1d02fe2000 r--p 00017000 08:06 1840062                    /lib/x86_64-linux-gnu/libpthread-2.17.so
7f1d02fe2000-7f1d02fe3000 rw-p 00018000 08:06 1840062                    /lib/x86_64-linux-gnu/libpthread-2.17.so
7f1d02fe3000-7f1d02fe7000 rw-p 00000000 00:00 0
7f1d02fe7000-7f1d02ffb000 r-xp 00000000 08:06 1838753                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1d02ffb000-7f1d031fb000 ---p 00014000 08:06 1838753                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1d031fb000-7f1d031fc000 r--p 00014000 08:06 1838753                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1d031fc000-7f1d031fd000 rw-p 00015000 08:06 1838753                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1d031fd000-7f1d0320b000 r-xp 00000000 08:06 524480                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f1d0320b000-7f1d0340a000 ---p 0000e000 08:06 524480                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f1d0340a000-7f1d0340b000 r--p 0000d000 08:06 524480                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f1d0340b000-7f1d0340c000 rw-p 0000e000 08:06 524480                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f1d0340c000-7f1d0350f000 r-xp 00000000 08:06 1840063                    /lib/x86_64-linux-gnu/libm-2.17.so
7f1d0350f000-7f1d0370f000 ---p 00103000 08:06 1840063                    /lib/x86_64-linux-gnu/libm-2.17.so
7f1d0370f000-7f1d03710000 r--p 00103000 08:06 1840063                    /lib/x86_64-linux-gnu/libm-2.17.so
7f1d03710000-7f1d03711000 rw-p 00104000 08:06 1840063                    /lib/x86_64-linux-gnu/libm-2.17.so
7f1d03711000-7f1d037f6000 r-xp 00000000 08:06 528325                     /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7f1d037f6000-7f1d039f5000 ---p 000e5000 08:06 528325                     /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7f1d039f5000-7f1d039fd000 r--p 000e4000 08:06 528325                     /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7f1d039fd000-7f1d039ff000 rw-p 000ec000 08:06 528325                     /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17
7f1d039ff000-7f1d03a14000 rw-p 00000000 00:00 0
7f1d03a14000-7f1d03a37000 r-xp 00000000 08:06 1840053                    /lib/x86_64-linux-gnu/ld-2.17.so
7f1d03c16000-7f1d03c1d000 rw-p 00000000 00:00 0
7f1d03c33000-7f1d03c36000 rw-p 00000000 00:00 0
7f1d03c36000-7f1d03c37000 r--p 00022000 08:06 1840053                    /lib/x86_64-linux-gnu/ld-2.17.so
7f1d03c37000-7f1d03c39000 rw-p 00023000 08:06 1840053                    /lib/x86_64-linux-gnu/ld-2.17.so
7fff93357000-7fff93379000 rw-p 00000000 00:00 0                          [stack]
7fff9337d000-7fff9337f000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)
[a5] Error building contigs with IDBA