Whole-Genome Shotgun Assembler / Bugs / #261 correct-olaps terminated

I am having what appears to be a similar issue: Any way to resolve this? This is CA 8.1.

*** buffer overflow detected ***: /share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x73e0f)[0x7f4a8c88be0f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f4a8c92371c]
/lib/x86_64-linux-gnu/libc.so.6(+0x10a5e0)[0x7f4a8c9225e0]
/share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps[0x403cb2]
/share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps[0x402597]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f4a8c839ec5]
/share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps[0x402c96]
======= Memory map: ========
00400000-00427000 r-xp 00000000 08:12 2282685                            /share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps
00626000-00627000 r--p 00026000 08:12 2282685                            /share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps
00627000-00628000 rw-p 00027000 08:12 2282685                            /share/MaSuRCA-2.3.2/CA/Linux-amd64/bin/correct-olaps
00628000-00636000 rw-p 00000000 00:00 0
0127f000-0d9ce000 rw-p 00000000 00:00 0                                  [heap]
7f4a7861f000-7f4a78620000 ---p 00000000 00:00 0
7f4a78620000-7f4a78e20000 rw-p 00000000 00:00 0
7f4a78e20000-7f4a78e21000 ---p 00000000 00:00 0
7f4a78e21000-7f4a79621000 rw-p 00000000 00:00 0
7f4a79621000-7f4a79622000 ---p 00000000 00:00 0
7f4a79622000-7f4a79e22000 rw-p 00000000 00:00 0
7f4a79e22000-7f4a79e23000 ---p 00000000 00:00 0
7f4a79e23000-7f4a8bda8000 rw-p 00000000 00:00 0
7f4a8bda8000-7f4a8bdab000 r-xp 00000000 08:12 1182764                    /lib/x86_64-linux-gnu/libdl-2.19.so
7f4a8bdab000-7f4a8bfaa000 ---p 00003000 08:12 1182764                    /lib/x86_64-linux-gnu/libdl-2.19.so
7f4a8bfaa000-7f4a8bfab000 r--p 00002000 08:12 1182764                    /lib/x86_64-linux-gnu/libdl-2.19.so
7f4a8bfab000-7f4a8bfac000 rw-p 00003000 08:12 1182764                    /lib/x86_64-linux-gnu/libdl-2.19.so
7f4a8bfb0000-7f4a8bfba000 r-xp 00000000 08:12 2894168                    /usr/lib/x86_64-linux-gnu/libnuma.so.1
7f4a8bfba000-7f4a8c1b9000 ---p 0000a000 08:12 2894168                    /usr/lib/x86_64-linux-gnu/libnuma.so.1
7f4a8c1b9000-7f4a8c1ba000 r--p 00009000 08:12 2894168                    /usr/lib/x86_64-linux-gnu/libnuma.so.1
7f4a8c1ba000-7f4a8c1bb000 rw-p 0000a000 08:12 2894168                    /usr/lib/x86_64-linux-gnu/libnuma.so.1
7f4a8c1c0000-7f4a8c1c9000 r-xp 00000000 08:12 2902341                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
7f4a8c1c9000-7f4a8c3c8000 ---p 00009000 08:12 2902341                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
7f4a8c3c8000-7f4a8c3c9000 r--p 00008000 08:12 2902341                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
7f4a8c3c9000-7f4a8c3ca000 rw-p 00009000 08:12 2902341                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.0
7f4a8c3d0000-7f4a8c40e000 r-xp 00000000 08:12 2885321                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.4.0
7f4a8c40e000-7f4a8c60e000 ---p 0003e000 08:12 2885321                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.4.0
7f4a8c60e000-7f4a8c60f000 r--p 0003e000 08:12 2885321                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.4.0
7f4a8c60f000-7f4a8c610000 rw-p 0003f000 08:12 2885321                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.4.0
7f4a8c610000-7f4a8c612000 r-xp 00000000 08:12 1180132                    /lib/x86_64-linux-gnu/libutil-2.19.so
7f4a8c612000-7f4a8c811000 ---p 00002000 08:12 1180132                    /lib/x86_64-linux-gnu/libutil-2.19.so
7f4a8c811000-7f4a8c812000 r--p 00001000 08:12 1180132                    /lib/x86_64-linux-gnu/libutil-2.19.so
7f4a8c812000-7f4a8c813000 rw-p 00002000 08:12 1180132                    /lib/x86_64-linux-gnu/libutil-2.19.so
7f4a8c818000-7f4a8c9d3000 r-xp 00000000 08:12 1182770                    /lib/x86_64-linux-gnu/libc-2.19.so
7f4a8c9d3000-7f4a8cbd3000 ---p 001bb000 08:12 1182770                    /lib/x86_64-linux-gnu/libc-2.19.so
7f4a8cbd3000-7f4a8cbd7000 r--p 001bb000 08:12 1182770                    /lib/x86_64-linux-gnu/libc-2.19.so
7f4a8cbd7000-7f4a8cbd9000 rw-p 001bf000 08:12 1182770                    /lib/x86_64-linux-gnu/libc-2.19.so
7f4a8cbd9000-7f4a8cbde000 rw-p 00000000 00:00 0
7f4a8cbe0000-7f4a8cbf6000 r-xp 00000000 08:12 1179661                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f4a8cbf6000-7f4a8cdf5000 ---p 00016000 08:12 1179661                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f4a8cdf5000-7f4a8cdf6000 rw-p 00015000 08:12 1179661                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7f4a8cdf8000-7f4a8cefd000 r-xp 00000000 08:12 1180124                    /lib/x86_64-linux-gnu/libm-2.19.so
7f4a8cefd000-7f4a8d0fc000 ---p 00105000 08:12 1180124                    /lib/x86_64-linux-gnu/libm-2.19.so
7f4a8d0fc000-7f4a8d0fd000 r--p 00104000 08:12 1180124                    /lib/x86_64-linux-gnu/libm-2.19.so
7f4a8d0fd000-7f4a8d0fe000 rw-p 00105000 08:12 1180124                    /lib/x86_64-linux-gnu/libm-2.19.so
7f4a8d100000-7f4a8d1e6000 r-xp 00000000 08:12 2884639                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f4a8d1e6000-7f4a8d3e5000 ---p 000e6000 08:12 2884639                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f4a8d3e5000-7f4a8d3ed000 r--p 000e5000 08:12 2884639                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f4a8d3ed000-7f4a8d3ef000 rw-p 000ed000 08:12 2884639                    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f4a8d3ef000-7f4a8d404000 rw-p 00000000 00:00 0
7f4a8d408000-7f4a8d421000 r-xp 00000000 08:12 1180130                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f4a8d421000-7f4a8d620000 ---p 00019000 08:12 1180130                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f4a8d620000-7f4a8d621000 r--p 00018000 08:12 1180130                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f4a8d621000-7f4a8d622000 rw-p 00019000 08:12 1180130                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7f4a8d622000-7f4a8d626000 rw-p 00000000 00:00 0
7f4a8d628000-7f4a8d77e000 r-xp 00000000 08:12 405785                     /usr/lib/openmpi/lib/libmpi.so.1.0.8
7f4a8d77e000-7f4a8d97d000 ---p 00156000 08:12 405785                     /usr/lib/openmpi/lib/libmpi.so.1.0.8
7f4a8d97d000-7f4a8d982000 r--p 00155000 08:12 405785                     /usr/lib/openmpi/lib/libmpi.so.1.0.8
7f4a8d982000-7f4a8d993000 rw-p 0015a000 08:12 405785                     /usr/lib/openmpi/lib/libmpi.so.1.0.8
7f4a8d993000-7f4a8d9a9000 rw-p 00000000 00:00 0
7f4a8d9b0000-7f4a8d9d3000 r-xp 00000000 08:12 1182767                    /lib/x86_64-linux-gnu/ld-2.19.so
7f4a8db0b000-7f4a8db0c000 rw-p 00000000 00:00 0
7f4a8dbc0000-7f4a8dbd2000 rw-p 00000000 00:00 0
7f4a8dbd2000-7f4a8dbd3000 r--p 00022000 08:12 1182767                    /lib/x86_64-linux-gnu/ld-2.19.so
7f4a8dbd3000-7f4a8dbd4000 rw-p 00023000 08:12 1182767                    /lib/x86_64-linux-gnu/ld-2.19.so
7f4a8dbd4000-7f4a8dbd6000 rw-p 00000000 00:00 0
7f4a8dbd6000-7f4a8dbda000 rw-p 00000000 00:00 0
7fff9e20a000-7fff9e22c000 rw-p 00000000 00:00 0                          [stack]
7fff9e400000-7fff9e402000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Brian Walenz - 2015-02-03

I can't reproduce this using valgrind on CA 8.2 (Masurca is using CA 6.1). It's possible we already fixed the problem.

Can either of you compile with debug symbols and run in a debugger, or best, with valgrind?

The alternative is to disable this module: doFragmentCorrection=0.

The impact should be relatively minor. All this module does is update the overlap error rate using guesses about where sequencing errors are. The masurca reads should be pretty clean.

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Brian Walenz - 2015-02-03

status: open --> pending

assigned_to: Brian Walenz
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

lpryszcz - 2018-03-20

Hi, I'm having similar issue in v2.3.4 and unfortunately your tweak doFragmentCorrection=0 doesn't work:/ Any other solutions?

Error line 55 of configuration file 'configuration.txt':
Invalid line 'doFragmentCorrection=0'

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Sergey Koren - 2018-03-20
  
  CA support ended in 2016. You should contact the MaSuRCA support team instead.
  
  Are you specifying doFragmentCorrection=0 in the MaSuRCA config? That is not going to work, it's a CA option not a MaSuRCA option. You need to run the CA command MaSuRCA is running but with the added parameter.
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - lpryszcz - 2018-03-21
    
    Thanks Sergey, it did the trick!
    https://github.com/alekseyzimin/masurca/issues/8#issuecomment-374885969
    
    Any idea why the error occured?
    
    Greetings from Waw!
    L.
    
    L.
    
    On 20 March 2018 at 17:37, Sergey Koren skoren@users.sourceforge.net
    wrote:
    
    CA support ended in 2016. You should contact the MaSuRCA support team
    instead.
    
    Are you specifying doFragmentCorrection=0 in the MaSuRCA config? That is
    not going to work, it's a CA option not a MaSuRCA option. You need to run
    the CA command MaSuRCA is running but with the added parameter.
    
    [bugs:#261] https://sourceforge.net/p/wgs-assembler/bugs/261/
    correct-olaps terminated*
    
    Status: pending
    Group: correction
    Created: Sat Oct 26, 2013 05:25 PM UTC by zhouqi
    Last Updated: Tue Mar 20, 2018 04:25 PM UTC
    Owner: Brian Walenz
    
    Hi,
    
    I’m using MaSuRCA assembler which takes CA6.0 as core and I got the some
    error message. Any input would be very much appreciated. My command is:
    
    runCA gkpFixInsertSizes=0 jellyfishHashSize=10000000000
    ovlRefBlockSize=1225516 ovlHashBlockSize=122551 ovlCorrBatchSize=40000000
    utgErrorRate=0.03 merylMemory=8192 ovlMemory=8GB stopAfter=unitigger
    ovlMerThreshold=75 bogBreakAtIntersections=0 unitigger=bog
    bogBadMateDepth=1000000 -p genome -d CA merylThreads=32 frgCorrThreads=1
    frgCorrConcurrency=48 cnsConcurrency=48 ovlCorrConcurrency=8
    ovlConcurrency=48 ovlThreads=1 doFragmentCorrection=1
    doOverlapBasedTrimming=1 doExtendClearRanges=2 ovlMerSize=22
    superReadSequences_shr.frg /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/Genomic_reads/Dmir.female.454.frg f5.cor.clean.frg
    m5.cor.clean.frg f1.cor.clean.frg f2.cor.clean.frg m2.cor.clean.frg 1>
    runCA0.out 2>&1
    
    and the error message is:
    
    ----------------------------------------END CONCURRENT Fri Oct 25
    21:36:34 2013 (64 seconds)
    Overlap correction job 1 (/jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/CA/3-overlapcorrection/0001)
    failed.
    ============================================================
    ====================
    
    runCA failed.
    
    Stack trace:
    
    at /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/runCA line 1121
    main::caFailure('1 overlap correction jobs failed; remove
    /jbods/data01/DATA/d...', undef) called at /jbods/data01/DATA/dmiran
    da/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/runCA
    line 3019
    main::overlapCorrection() called at /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/
    bin/runCA line 5343
    
    Failure message:
    
    1 overlap correction jobs failed; remove /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/MaSuRCA-2.1.0/CA/3-overlapcorrection
    /ovlcorr.sh (or run by hand) to try again
    
    buffer overflow detected *: /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps
    terminated
    ======= Backtrace: =========
    /lib/libc.so.6(
    
    fortify_fail+0x37)[0x7f474f7fcb47]
    /lib/libc.so.6(+0xfea00)[0x7f474f7fba00]
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x4030ee]
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x40520c]
    /lib/libc.so.6(libc_start_main+0xfe)[0x7f474f71bd8e]
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    new/MaSuRCA-2.1.0/CA/Linux-amd64/bin/correct-olaps[0x402279]
    ======= Memory map: ========
    00400000-00427000 r-xp 00000000 08:21 40083 /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-
    amd64/bin/correct-olaps
    00626000-00627000 r--p 00026000 08:21 40083 /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-
    amd64/bin/correct-olaps
    00627000-00628000 rw-p 00027000 08:21 40083 /jbods/data01/DATA/dmiranda/
    assemblyV3/D.miranda/MaSuRCA/new/MaSuRCA-2.1.0/CA/Linux-
    amd64/bin/correct-olaps
    00628000-00636000 rw-p 00000000 00:00 0
    01234000-68f4b000 rw-p 00000000 00:00 0 [heap]
    7f46690d9000-7f46690da000 ---p 00000000 00:00 0
    7f46690da000-7f4669ada000 rw-p 00000000 00:00 0
    7f4669ada000-7f4669adb000 ---p 00000000 00:00 0
    7f4669adb000-7f466a4db000 rw-p 00000000 00:00 0
    7f466a4db000-7f466a4dc000 ---p 00000000 00:00 0
    7f466a4dc000-7f466aedc000 rw-p 00000000 00:00 0
    7f466b8dd000-7f474f6fd000 rw-p 00000000 00:00 0
    7f474f6fd000-7f474f877000 r-xp 00000000 08:31 918102 /lib/libc-2.12.1.so
    7f474f877000-7f474fa77000 ---p 0017a000 08:31 918102 /lib/libc-2.12.1.so
    7f474fa77000-7f474fa7b000 r--p 0017a000 08:31 918102 /lib/libc-2.12.1.so
    7f474fa7b000-7f474fa7c000 rw-p 0017e000 08:31 918102 /lib/libc-2.12.1.so
    7f474fa7c000-7f474fa81000 rw-p 00000000 00:00 0
    7f474fa81000-7f474fa96000 r-xp 00000000 08:31 917564 /lib/libgcc_s.so.1
    7f474fa96000-7f474fc95000 ---p 00015000 08:31 917564 /lib/libgcc_s.so.1
    7f474fc95000-7f474fc96000 r--p 00014000 08:31 917564 /lib/libgcc_s.so.1
    7f474fc96000-7f474fc97000 rw-p 00015000 08:31 917564 /lib/libgcc_s.so.1
    7f474fc97000-7f474fd19000 r-xp 00000000 08:31 918106 /lib/libm-2.12.1.so
    7f474fd19000-7f474ff18000 ---p 00082000 08:31 918106 /lib/libm-2.12.1.so
    7f474ff18000-7f474ff19000 r--p 00081000 08:31 918106 /lib/libm-2.12.1.so
    7f474ff19000-7f474ff1a000 rw-p 00082000 08:31 918106 /lib/libm-2.12.1.so
    7f474ff1a000-7f4750002000 r-xp 00000000 08:31 14684593
    /usr/lib/libstdc++.so.6.0.14
    7f4750002000-7f4750201000 ---p 000e8000 08:31 14684593
    /usr/lib/libstdc++.so.6.0.14
    7f4750201000-7f4750209000 r--p 000e7000 08:31 14684593
    /usr/lib/libstdc++.so.6.0.14
    7f4750209000-7f475020b000 rw-p 000ef000 08:31 14684593
    /usr/lib/libstdc++.so.6.0.14
    7f475020b000-7f4750220000 rw-p 00000000 00:00 0
    7f4750220000-7f4750248000 r-xp 00000000 08:21 34381
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
    7f4750248000-7f4750448000 ---p 00028000 08:21 34381
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
    7f4750448000-7f4750449000 r--p 00028000 08:21 34381
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
    7f4750449000-7f475044a000 rw-p 00029000 08:21 34381
    /jbods/data01/DATA/dmiranda/assemblyV3/D.miranda/MaSuRCA/
    MaSuRCA-2.1.0/lib/libjellyfish-2.0.so.2.0.0
    7f475044a000-7f4750462000 r-xp 00000000 08:31 918123 /lib/
    libpthread-2.12.1.so
    7f4750462000-7f4750661000 ---p 00018000 08:31 918123 /lib/
    libpthread-2.12.1.so
    7f4750661000-7f4750662000 r--p 00017000 08:31 918123 /lib/
    libpthread-2.12.1.so
    7f4750662000-7f4750663000 rw-p 00018000 08:31 918123 /lib/
    libpthread-2.12.1.so
    7f4750663000-7f4750667000 rw-p 00000000 00:00 0
    7f4750667000-7f4750687000 r-xp 00000000 08:31 918051 /lib/ld-2.12.1.so
    7f475085b000-7f4750861000 rw-p 00000000 00:00 0
    7f4750878000-7f4750887000 rw-p 00000000 00:00 0
    7f4750887000-7f4750888000 r--p 00020000 08:31 918051 /lib/ld-2.12.1.so
    7f4750888000-7f4750889000 rw-p 00021000 08:31 918051 /lib/ld-2.12.1.so
    7f4750889000-7f475088a000 rw-p 00000000 00:00 0
    7fff824ab000-7fff824cd000 rw-p 00000000 00:00 0 [stack]
    7fff82583000-7fff82584000 r-xp 00000000 00:00 0 [vdso]
    ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
    
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    Related
    
    Bugs: #261
    
    alternate
    
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