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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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buffer overflow detected ***: /usr/local/bin/../libexec/denovogear/dng-dnm terminated #288

Closed vgastaldi closed 4 years ago

vgastaldi commented 5 years ago

Dear all,

I've been trying to use dng dnm function with a number of trios, but for some of them I keep getting a buffer overflow error.

I ran "dng dnm auto -p FAM_V10.ped -v FAM_V10_SNP_INDEL_recalibrated_raw_variants.vcf" and this is the backtrace:

*** buffer overflow detected ***: /usr/local/bin/../libexec/denovogear/dng-dnm terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f2774b517e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f2774bf315c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7f2774bf1160]
/lib/x86_64-linux-gnu/libc.so.6(+0x1164b2)[0x7f2774bf04b2]
/usr/local/bin/../libexec/denovogear/dng-dnm(_Z16writeToSNPObjectP12snp_object_tPK9bcf_hdr_tP6bcf1_tPiiiRiii+0x210)[0x443450]
/usr/local/bin/../libexec/denovogear/dng-dnm(_Z10bcf_2qcallPK9bcf_hdr_tP6bcf1_t4TrioP12snp_object_tS6_S6_P7indel_tS8_S8_Rii+0xb28)[0x444518]
/usr/local/bin/../libexec/denovogear/dng-dnm(_ZN3dng4task3DNMclERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS0_3dnm5arg_tE+0x931)[0x41cf71]
/usr/local/bin/../libexec/denovogear/dng-dnm(main+0xf8)[0x41b168]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f2774afa830]
/usr/local/bin/../libexec/denovogear/dng-dnm(_start+0x29)[0x41b539]
======= Memory map: ========
00400000-004da000 r-xp 00000000 08:07 20189433                           /usr/local/libexec/denovogear/dng-dnm
006d9000-006da000 r--p 000d9000 08:07 20189433                           /usr/local/libexec/denovogear/dng-dnm
006da000-006db000 rw-p 000da000 08:07 20189433                           /usr/local/libexec/denovogear/dng-dnm
006db000-006dc000 rw-p 00000000 00:00 0 
0101f000-010a2000 rw-p 00000000 00:00 0                                  [heap]
7f2774ada000-7f2774c9a000 r-xp 00000000 08:07 266496                     /lib/x86_64-linux-gnu/libc-2.23.so
7f2774c9a000-7f2774e9a000 ---p 001c0000 08:07 266496                     /lib/x86_64-linux-gnu/libc-2.23.so
7f2774e9a000-7f2774e9e000 r--p 001c0000 08:07 266496                     /lib/x86_64-linux-gnu/libc-2.23.so
7f2774e9e000-7f2774ea0000 rw-p 001c4000 08:07 266496                     /lib/x86_64-linux-gnu/libc-2.23.so
7f2774ea0000-7f2774ea4000 rw-p 00000000 00:00 0 
7f2774ea4000-7f2774ebc000 r-xp 00000000 08:07 266495                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7f2774ebc000-7f27750bb000 ---p 00018000 08:07 266495                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7f27750bb000-7f27750bc000 r--p 00017000 08:07 266495                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7f27750bc000-7f27750bd000 rw-p 00018000 08:07 266495                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7f27750bd000-7f27750c1000 rw-p 00000000 00:00 0 
7f27750c1000-7f27750d7000 r-xp 00000000 08:07 266602                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f27750d7000-7f27752d6000 ---p 00016000 08:07 266602                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f27752d6000-7f27752d7000 rw-p 00015000 08:07 266602                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f27752d7000-7f27753df000 r-xp 00000000 08:07 262393                     /lib/x86_64-linux-gnu/libm-2.23.so
7f27753df000-7f27755de000 ---p 00108000 08:07 262393                     /lib/x86_64-linux-gnu/libm-2.23.so
7f27755de000-7f27755df000 r--p 00107000 08:07 262393                     /lib/x86_64-linux-gnu/libm-2.23.so
7f27755df000-7f27755e0000 rw-p 00108000 08:07 262393                     /lib/x86_64-linux-gnu/libm-2.23.so
7f27755e0000-7f2775752000 r-xp 00000000 08:07 19794717                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2775752000-7f2775952000 ---p 00172000 08:07 19794717                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f2775952000-7f277595c000 r--p 00172000 08:07 19794717                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f277595c000-7f277595e000 rw-p 0017c000 08:07 19794717                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f277595e000-7f2775962000 rw-p 00000000 00:00 0 
7f2775962000-7f2775965000 r-xp 00000000 08:07 19799838                   /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0
7f2775965000-7f2775b64000 ---p 00003000 08:07 19799838                   /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0
7f2775b64000-7f2775b65000 r--p 00002000 08:07 19799838                   /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0
7f2775b65000-7f2775b66000 rw-p 00003000 08:07 19799838                   /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0
7f2775b66000-7f2775b7d000 r-xp 00000000 08:07 19799836                   /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0
7f2775b7d000-7f2775d7c000 ---p 00017000 08:07 19799836                   /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0
7f2775d7c000-7f2775d7d000 r--p 00016000 08:07 19799836                   /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0
7f2775d7d000-7f2775d7e000 rw-p 00017000 08:07 19799836                   /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0
7f2775d7e000-7f2775df8000 r-xp 00000000 08:07 19792882                   /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0
7f2775df8000-7f2775ff8000 ---p 0007a000 08:07 19792882                   /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0
7f2775ff8000-7f2775ffb000 r--p 0007a000 08:07 19792882                   /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0
7f2775ffb000-7f2775ffc000 rw-p 0007d000 08:07 19792882                   /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0
7f2775ffc000-7f2776015000 r-xp 00000000 08:07 262314                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2776015000-7f2776214000 ---p 00019000 08:07 262314                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2776214000-7f2776215000 r--p 00018000 08:07 262314                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2776215000-7f2776216000 rw-p 00019000 08:07 262314                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f2776216000-7f277623c000 r-xp 00000000 08:07 266494                     /lib/x86_64-linux-gnu/ld-2.23.so
7f2776413000-7f277641b000 rw-p 00000000 00:00 0 
7f277643a000-7f277643b000 rw-p 00000000 00:00 0 
7f277643b000-7f277643c000 r--p 00025000 08:07 266494                     /lib/x86_64-linux-gnu/ld-2.23.so
7f277643c000-7f277643d000 rw-p 00026000 08:07 266494                     /lib/x86_64-linux-gnu/ld-2.23.so
7f277643d000-7f277643e000 rw-p 00000000 00:00 0 
7ffe8866c000-7ffe886a9000 rw-p 00000000 00:00 0                          [stack]
7ffe887fb000-7ffe887fe000 r--p 00000000 00:00 0                          [vvar]
7ffe887fe000-7ffe88800000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

What can I do to avoid/solve this? I attached the files if you want to reproduce it. fam_v10.zip

Thank you.

vgastaldi commented 5 years ago

Just noticed that when I build with "-DCMAKE_BUILD_TYPE=Debug" it works.

reedacartwright commented 5 years ago

@jgarc111 Can you look into this crash after the semester is over?

jgarciamesa commented 5 years ago

Of course, I will do.

jgarciamesa commented 4 years ago

Closing since I understand PR #295 fixed this. Feel free to reopen if issue persists.