tg_index buffer overflow

2011-10-31
2013-04-18
  • jdmontenegroc
    jdmontenegroc
    2011-10-31

    Dear James,

    I have just compiled from source the latest realease of the Staden Package which includes GAP5 on Ubuntu 11.04 platform with 8GB RAM and 300GB free space (i7).
    However after filtering the caf fileobtained with MIRA 3.0 I tried tg_index and found this problem:

    g_index: Short Read Alignment Indexer, version 1.2.11

    Author: James Bonfield (jkb@sanger.ac.uk)
            2007-2011, Wellcome Trust Sanger Institute

    Selecting output database filename 11A_50X_CJ_F.0
    Processing CAF file 11A_50X_CJ_F.caf
    Loading 11A_50X_CJ_F.caf…
    Input summary
    Reads 16076
    Quality 16082
    Contigs 6
    Bases 16082
    R + C 16082
    Indexed in 0.169169 seconds
    Loading …
    *** buffer overflow detected ***: tg_index.bin terminated
    ======= Backtrace: =========
    /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)
    /lib/x86_64-linux-gnu/libc.so.6(+0xfd0f0)
    /usr/local/bin/../lib/staden/libtgap.so(contig_set_name+0x84)
    /usr/local/bin/../lib/staden/libtgap.so(contig_new+0x89)
    /usr/local/bin/../lib/staden/libgap5.so(create_new_contig+0x7b)
    /usr/local/bin/../lib/staden/libgap5.so(parse_caf+0x417)
    tg_index.bin(main+0x6e5)
    /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)
    tg_index.bin
    ======= Memory map: ========
    00400000-00403000 r-xp 00000000 08:04 17401915                           /usr/local/bin/tg_index.bin
    00603000-00604000 r-p 00003000 08:04 17401915                           /usr/local/bin/tg_index.bin
    00604000-00605000 rw-p 00004000 08:04 17401915                           /usr/local/bin/tg_index.bin
    023bc000-02422000 rw-p 00000000 00:00 0                                 
    7f9b82a1c000-7f9b82a31000 r-xp 00000000 08:04 20725836                   /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f9b82a31000-7f9b82c30000 --p 00015000 08:04 20725836                   /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f9b82c30000-7f9b82c31000 r-p 00014000 08:04 20725836                   /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f9b82c31000-7f9b82c32000 rw-p 00015000 08:04 20725836                   /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f9b82c56000-7f9b8311c000 rw-p 00000000 00:00 0
    7f9b8311c000-7f9b83121000 r-xp 00000000 08:04 17203755                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
    7f9b83121000-7f9b83320000 --p 00005000 08:04 17203755                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
    7f9b83320000-7f9b83321000 r-p 00004000 08:04 17203755                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
    7f9b83321000-7f9b83322000 rw-p 00005000 08:04 17203755                   /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
    7f9b83322000-7f9b83324000 r-xp 00000000 08:04 17203739                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
    7f9b83324000-7f9b83523000 --p 00002000 08:04 17203739                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
    7f9b83523000-7f9b83524000 r-p 00001000 08:04 17203739                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
    7f9b83524000-7f9b83525000 rw-p 00002000 08:04 17203739                   /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
    7f9b83525000-7f9b83540000 r-xp 00000000 08:04 17203763                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
    7f9b83540000-7f9b8373f000 --p 0001b000 08:04 17203763                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
    7f9b8373f000-7f9b83740000 r-p 0001a000 08:04 17203763                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
    7f9b83740000-7f9b83741000 rw-p 0001b000 08:04 17203763                   /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
    7f9b83741000-7f9b83767000 r-xp 00000000 08:04 20725826                   /lib/x86_64-linux-gnu/libpng12.so.0.44.0
    7f9b83767000-7f9b83966000 --p 00026000 08:04 20725826                   /lib/x86_64-linux-gnu/libpng12.so.0.44.0
    7f9b83966000-7f9b83967000 r-p 00025000 08:04 20725826                   /lib/x86_64-linux-gnu/libpng12.so.0.44.0
    7f9b83967000-7f9b83968000 rw-p 00026000 08:04 20725826                   /lib/x86_64-linux-gnu/libpng12.so.0.44.0
    7f9b83968000-7f9b83989000 r-xp 00000000 08:04 17091021                   /usr/lib/liblzma.so.2.0.0
    7f9b83989000-7f9b83b88000 --p 00021000 08:04 17091021                   /usr/lib/liblzma.so.2.0.0
    7f9b83b88000-7f9b83b89000 r-p 00020000 08:04 17091021                   /usr/lib/liblzma.so.2.0.0
    7f9b83b89000-7f9b83b8a000 rw-p 00021000 08:04 17091021                   /usr/lib/liblzma.so.2.0.0
    7f9b83b8a000-7f9b83d14000 r-xp 00000000 08:04 20725835                   /lib/x86_64-linux-gnu/libc-2.13.so
    7f9b83d14000-7f9b83f13000 --p 0018a000 08:04 20725835                   /lib/x86_64-linux-gnu/libc-2.13.so
    7f9b83f13000-7f9b83f17000 r-p 00189000 08:04 20725835                   /lib/x86_64-linux-gnu/libc-2.13.so
    7f9b83f17000-7f9b83f18000 rw-p 0018d000 08:04 20725835                   /lib/x86_64-linux-gnu/libc-2.13.so
    7f9b83f18000-7f9b83f1e000 rw-p 00000000 00:00 0
    7f9b83f1e000-7f9b83f51000 r-xp 00000000 08:04 17401326                   /usr/local/lib/libstaden-read.so.1.1.3
    7f9b83f51000-7f9b84150000 --p 00033000 08:04 17401326                   /usr/local/lib/libstaden-read.so.1.1.3
    7f9b84150000-7f9b84151000 r-p 00032000 08:04 17401326                   /usr/local/lib/libstaden-read.so.1.1.3
    7f9b84151000-7f9b84155000 rw-p 00033000 08:04 17401326                   /usr/local/lib/libstaden-read.so.1.1.3
    7f9b84155000-7f9b84198000 rw-p 00000000 00:00 0
    7f9b84198000-7f9b841a1000 r-xp 00000000 08:04 18106572                   /usr/local/lib/staden/libmisc.so
    7f9b841a1000-7f9b843a0000 --p 00009000 08:04 18106572                   /usr/local/lib/staden/libmisc.so
    7f9b843a0000-7f9b843a1000 r-p 00008000 08:04 18106572                   /usr/local/lib/staden/libmisc.so
    7f9b843a1000-7f9b843a2000 rw-p 00009000 08:04 18106572                   /usr/local/lib/staden/libmisc.so
    7f9b843a2000-7f9b843a4000 rw-p 00000000 00:00 0
    7f9b843a4000-7f9b84428000 r-xp 00000000 08:04 20725860                   /lib/x86_64-linux-gnu/libm-2.13.so
    7f9b84428000-7f9b84627000 --p 00084000 08:04 20725860                   /lib/x86_64-linux-gnu/libm-2.13.so
    7f9b84627000-7f9b84628000 r-p 00083000 08:04 20725860                   /lib/x86_64-linux-gnu/libm-2.13.so
    7f9b84628000-7f9b84629000 rw-p 00084000 08:04 20725860                   /lib/x86_64-linux-gnu/libm-2.13.so
    7f9b84629000-7f9b84641000 r-xp 00000000 08:04 20725897                   /lib/x86_64-linux-gnu/libpthread-2.13.so
    7f9b84641000-7f9b84841000 --p 00018000 08:04 20725897                   /lib/x86_64-linux-gnu/libpthread-2.13.so
    7f9b84841000-7f9b84842000 r-p 00018000 08:04 20725897                   /lib/x86_64-linux-gnu/libpthread-2.13.so
    7f9b84842000-7f9b84843000 rw-p 00019000 08:04 20725897                   /lib/x86_64-linux-gnu/libpthread-2.13.so
    7f9b84843000-7f9b84847000 rw-p 00000000 00:00 0
    7f9b84847000-7f9b84849000 r-xp 00000000 08:04 20725854                   /lib/x86_64-linux-gnu/libdl-2.13.so
    7f9b84849000-7f9b84a49000 --p 00002000 08:04 20725854                   /lib/x86_64-linux-gnu/libdl-2.13.sozsh: abort      tg_index -C 11A_50X_CJ_F.caf

    Do you have any idea how to solve this?

    What is going on? Sorry for such a long mail.

    Regards,

    Juan Montenegro

     
  • John Nash
    John Nash
    2011-10-31

    I followed you over from the MIRA list to try and help out here.  I'm running tg_index / gap5 on Ubuntu 11.04 (amongst several other platforms).  It runs fine here. One thing I noticed is that you are using:

    g_index: Short Read Alignment Indexer, version 1.2.11

    My version says:

    g_index: Short Read Alignment Indexer, version 1.2.13-rexported

    Maybe you could checkout the latest version from svn and re-make it just to make sure nothing has changed between our versions…

    John

     
  • jdmontenegroc
    jdmontenegroc
    2011-10-31

    Hi,

    I have just installed svn but cannot import g_index, cannot find the repository direction.  Could you please point in the right direction?

    Juan Montenegro

     
  • James Bonfield
    James Bonfield
    2011-11-01

    Try

        svn co https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk staden.trunk

    and then build within there. I do despately need to create a new official release, but every time I was about to do it some other hideous bug cropped up. It seems to have settled down now so I should probably take the time to go for it. At the very least it's easy to produce a tarball, although updating all the documentation and release notes takes longer.

    James

     
  • jdmontenegroc
    jdmontenegroc
    2011-11-02

    Hi James,
    I have just downloaded the staden.trunk, but it has no configure to run.  it only have bootstrap.  Could i just copy the configure file from another version of staden and use it instead?

    Regards,

    Juan Montenegro

     
  • James Bonfield
    James Bonfield
    2011-11-02

    Probably, but you may need some other bits too such as aclocal.m4.

    The bootstrap uses autoconf to generate the configure script for you though which is the recommended mode (provided you have it installed).

     
  • jdmontenegroc
    jdmontenegroc
    2011-11-02

    So I would have to execute ./bootstrap to generate the configure file and then run ./configure && make, right?

     
  • John Nash
    John Nash
    2011-11-02

    Yes - that works for me. I do:

    ./bootstrap
    ./configure -with options
    make
    make install

     
  • jdmontenegroc
    jdmontenegroc
    2011-11-02

    Thank you very much,

    That solved the problem with tg_index, now everything is working fine.