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  • OrthAgogue Buffer Overflow Error

    Hello folks,

    I'm trying to use a piece of software called OrthAgogue (https://code.google.com/p/orthagogue/wiki/manual).

    It's supposed to be similar to OrthoMCL but without the unpleasant SQL part.

    However, I'm having some trouble and can't find help anywhere online. Any help would be massively appreciated.

    On attempting to run orthAgogue with:

    orthAgogue all-vs-all_test -t 1 -p 2

    I received a message:

    *** buffer overflow detected ***: orthAgogue terminated

    The following was beneath this message:

    ======= Backtrace: =========
    /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f1c38b1d08c]
    /lib/x86_64-linux-gnu/libc.so.6(+0x111020)[0x7f1c38b1c020]
    /lib/x86_64-linux-gnu/libc.so.6(+0x1104a9)[0x7f1c38b1b4a9]
    /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xdb)[0x7f1c38a87a3b]
    /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x37cf)[0x7f1c38a57f4f]
    /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x94)[0x7f1c38b1b544]
    /lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f1c38b1b48d]
    orthAgogue(_ZN11log_builder13get_file_sizeEPciPKc+0xb7)[0x414247]
    orthAgogue(_ZN13blast_parsing13start_parsingEP11log_builderi+0x57)[0x415887]
    orthAgogue(_ZN13blast_parsing13start_parsingEP11log_builderR12bp_containeri+0x1b)[0x41605b]
    orthAgogue(_Z20main_operation_turboiPPc+0x1f0)[0x4100f0]
    orthAgogue(main+0x9)[0x40fe09]
    /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f1c38a2cde5]
    orthAgogue[0x40fe39]
    ======= Memory map: ========
    00400000-00451000 r-xp 00000000 08:01 17972919 /usr/bin/orthAgogue
    00651000-00652000 r--p 00051000 08:01 17972919 /usr/bin/orthAgogue
    00652000-00653000 rw-p 00052000 08:01 17972919 /usr/bin/orthAgogue
    01760000-01781000 rw-p 00000000 00:00 0 [heap]
    7f1c387ee000-7f1c38805000 r-xp 00000000 08:01 26870242 /lib/x86_64-linux-gnu/libpthread-2.17.so
    7f1c38805000-7f1c38a05000 ---p 00017000 08:01 26870242 /lib/x86_64-linux-gnu/libpthread-2.17.so
    7f1c38a05000-7f1c38a06000 r--p 00017000 08:01 26870242 /lib/x86_64-linux-gnu/libpthread-2.17.so
    7f1c38a06000-7f1c38a07000 rw-p 00018000 08:01 26870242 /lib/x86_64-linux-gnu/libpthread-2.17.so
    7f1c38a07000-7f1c38a0b000 rw-p 00000000 00:00 0
    7f1c38a0b000-7f1c38bc8000 r-xp 00000000 08:01 26870240 /lib/x86_64-linux-gnu/libc-2.17.so
    7f1c38bc8000-7f1c38dc8000 ---p 001bd000 08:01 26870240 /lib/x86_64-linux-gnu/libc-2.17.so
    7f1c38dc8000-7f1c38dcc000 r--p 001bd000 08:01 26870240 /lib/x86_64-linux-gnu/libc-2.17.so
    7f1c38dcc000-7f1c38dce000 rw-p 001c1000 08:01 26870240 /lib/x86_64-linux-gnu/libc-2.17.so
    7f1c38dce000-7f1c38dd3000 rw-p 00000000 00:00 0
    7f1c38dd3000-7f1c38de8000 r-xp 00000000 08:01 26870320 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f1c38de8000-7f1c38fe7000 ---p 00015000 08:01 26870320 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f1c38fe7000-7f1c38fe8000 r--p 00014000 08:01 26870320 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f1c38fe8000-7f1c38fe9000 rw-p 00015000 08:01 26870320 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f1c38fe9000-7f1c390ec000 r-xp 00000000 08:01 26870226 /lib/x86_64-linux-gnu/libm-2.17.so
    7f1c390ec000-7f1c392eb000 ---p 00103000 08:01 26870226 /lib/x86_64-linux-gnu/libm-2.17.so
    7f1c392eb000-7f1c392ec000 r--p 00102000 08:01 26870226 /lib/x86_64-linux-gnu/libm-2.17.so
    7f1c392ec000-7f1c392ed000 rw-p 00103000 08:01 26870226 /lib/x86_64-linux-gnu/libm-2.17.so
    7f1c392ed000-7f1c393d3000 r-xp 00000000 08:01 17957093 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18
    7f1c393d3000-7f1c395d2000 ---p 000e6000 08:01 17957093 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18
    7f1c395d2000-7f1c395da000 r--p 000e5000 08:01 17957093 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18
    7f1c395da000-7f1c395dc000 rw-p 000ed000 08:01 17957093 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18
    7f1c395dc000-7f1c395f1000 rw-p 00000000 00:00 0
    7f1c395f1000-7f1c39620000 r-xp 00000000 08:01 17964665 /usr/lib/libtbb.so.2
    7f1c39620000-7f1c3981f000 ---p 0002f000 08:01 17964665 /usr/lib/libtbb.so.2
    7f1c3981f000-7f1c39821000 r--p 0002e000 08:01 17964665 /usr/lib/libtbb.so.2
    7f1c39821000-7f1c39823000 rw-p 00030000 08:01 17964665 /usr/lib/libtbb.so.2
    7f1c39823000-7f1c39825000 rw-p 00000000 00:00 0
    7f1c39825000-7f1c39840000 r-xp 00000000 08:01 17972897 /usr/lib/libcmph.so.0.0.0
    7f1c39840000-7f1c39a3f000 ---p 0001b000 08:01 17972897 /usr/lib/libcmph.so.0.0.0
    7f1c39a3f000-7f1c39a40000 r--p 0001a000 08:01 17972897 /usr/lib/libcmph.so.0.0.0
    7f1c39a40000-7f1c39a41000 rw-p 0001b000 08:01 17972897 /usr/lib/libcmph.so.0.0.0
    7f1c39a41000-7f1c39a64000 r-xp 00000000 08:01 26870229 /lib/x86_64-linux-gnu/ld-2.17.so
    7f1c39c36000-7f1c39c3c000 rw-p 00000000 00:00 0
    7f1c39c60000-7f1c39c63000 rw-p 00000000 00:00 0
    7f1c39c63000-7f1c39c64000 r--p 00022000 08:01 26870229 /lib/x86_64-linux-gnu/ld-2.17.so
    7f1c39c64000-7f1c39c66000 rw-p 00023000 08:01 26870229 /lib/x86_64-linux-gnu/ld-2.17.so
    7fff7975f000-7fff79780000 rw-p 00000000 00:00 0 [stack]
    7fff797fe000-7fff79800000 r-xp 00000000 00:00 0 [vdso]
    ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
    Aborted

  • #2
    I sorted this by pestering a bioinformatician I know that uses orthAgogue.

    I basically entered the command incorrectly.

    Where this produced an error:

    orthAgogue all-vs-all_test -t 1 -p 2

    This produces an actual output:

    orthAgogue -i all-vs-all.tsv -b -e 6 -O /home/jwk9/Independent_Project/Test/All_Proteins/Results

    I missed out the "-i" before the input blast file.

    Just to save anybody (as braindead as myself) from potential struggle...

    Comment

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