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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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Aborted (core dumped) calling trio buffer overflow #290

Closed DataOmics76 closed 5 years ago

DataOmics76 commented 5 years ago

Hi again! Sorry for disturb again

I follow the instructions and get the next error, think maybe something similar as another thread?

Thanks!

samtools mpileup -gDf hg38.fa 02.bam 06.bam 08.bam > bcffile.bcf

/dng dnm auto --ped trioDNV.ped --bcf bcffile.bcf > out.bcf

Created SNP lookup table First mrate: 1 last: 1 First code: 6 last: 6 First target string: AA/AA/AA last: TT/TT/TT First tref: 0.0002388 last: 0.99301

Created indel lookup table First code: 6 last: 6 First target string: RR/RR/RR last: DD/DD/DD First prior: 0.05 last: 0.114

Created paired lookup table First target string: AA/AA last: TT/TT First prior 1 last: 1 buffer overflow detected : /home/cri/dng/bin/../libexec/denovogear/dng-dnm terminated ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f04a4ce67e5] /lib/x86_64-linux-gnu/libc.so.6(fortify_fail+0x5c)[0x7f04a4d8815c] /lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7f04a4d86160] /lib/x86_64-linux-gnu/libc.so.6(+0x1164b2)[0x7f04a4d854b2] /home/cri/dng/bin/../libexec/denovogear/dng-dnm(_Z9parse_pedNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorI4TrioSaIS6_EERS5_I4PairSaISA_EE+0x1b3)[0x439673] /home/cri/dng/bin/../libexec/denovogear/dng-dnm(_ZN3dng4task3DNMclERNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS0_3dnm5arg_tE+0x432)[0x413ad2] /home/cri/dng/bin/../libexec/denovogear/dng-dnm(main+0xf8)[0x4121d8] /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xf0)[0x7f04a4c8f830] /home/cri/dng/bin/../libexec/denovogear/dng-dnm(_start+0x29)[0x412599] ======= Memory map: ======== 00400000-00446000 r-xp 00000000 08:01 10226206 /home/cri/dng/libexec/denovogear/dng-dnm 00645000-00646000 r--p 00045000 08:01 10226206 /home/cri/dng/libexec/denovogear/dng-dnm 00646000-00647000 rw-p 00046000 08:01 10226206 /home/cri/dng/libexec/denovogear/dng-dnm 020f4000-02126000 rw-p 00000000 00:00 0 [heap] 7f04a41ef000-7f04a41f2000 r-xp 00000000 08:01 2883788 /lib/x86_64-linux-gnu/libdl-2.23.so 7f04a41f2000-7f04a43f1000 ---p 00003000 08:01 2883788 /lib/x86_64-linux-gnu/libdl-2.23.so 7f04a43f1000-7f04a43f2000 r--p 00002000 08:01 2883788 /lib/x86_64-linux-gnu/libdl-2.23.so 7f04a43f2000-7f04a43f3000 rw-p 00003000 08:01 2883788 /lib/x86_64-linux-gnu/libdl-2.23.so 7f04a43f7000-7f04a440f000 r-xp 00000000 08:01 2883644 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f04a440f000-7f04a460e000 ---p 00018000 08:01 2883644 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f04a460e000-7f04a460f000 r--p 00017000 08:01 2883644 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f04a460f000-7f04a4610000 rw-p 00018000 08:01 2883644 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f04a4610000-7f04a4614000 rw-p 00000000 00:00 0 7f04a4617000-7f04a4638000 r-xp 00000000 08:01 2888180 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f04a4638000-7f04a4837000 ---p 00021000 08:01 2888180 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f04a4837000-7f04a4838000 r--p 00020000 08:01 2888180 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f04a4838000-7f04a4839000 rw-p 00021000 08:01 2888180 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f04a483f000-7f04a484e000 r-xp 00000000 08:01 2888112 /lib/x86_64-linux-gnu/libbz2.so.1.0.4 7f04a484e000-7f04a4a4d000 ---p 0000f000 08:01 2888112 /lib/x86_64-linux-gnu/libbz2.so.1.0.4 7f04a4a4d000-7f04a4a4e000 r--p 0000e000 08:01 2888112 /lib/x86_64-linux-gnu/libbz2.so.1.0.4 7f04a4a4e000-7f04a4a4f000 rw-p 0000f000 08:01 2888112 /lib/x86_64-linux-gnu/libbz2.so.1.0.4 7f04a4a4f000-7f04a4a68000 r-xp 00000000 08:01 2948198 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f04a4a68000-7f04a4c67000 ---p 00019000 08:01 2948198 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f04a4c67000-7f04a4c68000 r--p 00018000 08:01 2948198 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f04a4c68000-7f04a4c69000 rw-p 00019000 08:01 2948198 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f04a4c6f000-7f04a4e2f000 r-xp 00000000 08:01 2883656 /lib/x86_64-linux-gnu/libc-2.23.so 7f04a4e2f000-7f04a502f000 ---p 001c0000 08:01 2883656 /lib/x86_64-linux-gnu/libc-2.23.so 7f04a502f000-7f04a5033000 r--p 001c0000 08:01 2883656 /lib/x86_64-linux-gnu/libc-2.23.so 7f04a5033000-7f04a5035000 rw-p 001c4000 08:01 2883656 /lib/x86_64-linux-gnu/libc-2.23.so 7f04a5035000-7f04a5039000 rw-p 00000000 00:00 0 7f04a503f000-7f04a5056000 r-xp 00000000 08:01 2883650 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f04a5056000-7f04a5255000 ---p 00017000 08:01 2883650 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f04a5255000-7f04a5256000 r--p 00016000 08:01 2883650 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f04a5256000-7f04a5257000 rw-p 00017000 08:01 2883650 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f04a5257000-7f04a535f000 r-xp 00000000 08:01 2883615 /lib/x86_64-linux-gnu/libm-2.23.so 7f04a535f000-7f04a555e000 ---p 00108000 08:01 2883615 /lib/x86_64-linux-gnu/libm-2.23.so 7f04a555e000-7f04a555f000 r--p 00107000 08:01 2883615 /lib/x86_64-linux-gnu/libm-2.23.so 7f04a555f000-7f04a5560000 rw-p 00108000 08:01 2883615 /lib/x86_64-linux-gnu/libm-2.23.so 7f04a5567000-7f04a56e3000 r-xp 00000000 08:01 4325472 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 7f04a56e3000-7f04a58e3000 ---p 0017c000 08:01 4325472 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 7f04a58e3000-7f04a58ed000 r--p 0017c000 08:01 4325472 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 7f04a58ed000-7f04a58ef000 rw-p 00186000 08:01 4325472 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 7f04a58ef000-7f04a58f3000 rw-p 00000000 00:00 0 7f04a58f7000-7f04a58fb000 r-xp 00000000 08:01 4346739 /usr/lib/libboost_system.so.1.68.0 7f04a58fb000-7f04a5afa000 ---p 00004000 08:01 4346739 /usr/lib/libboost_system.so.1.68.0 7f04a5afa000-7f04a5afb000 r--p 00003000 08:01 4346739 /usr/lib/libboost_system.so.1.68.0 7f04a5afb000-7f04a5afc000 rw-p 00004000 08:01 4346739 /usr/lib/libboost_system.so.1.68.0 7f04a5aff000-7f04a5b18000 r-xp 00000000 08:01 4346755 /usr/lib/libboost_filesystem.so.1.68.0 7f04a5b18000-7f04a5d18000 ---p 00019000 08:01 4346755 /usr/lib/libboost_filesystem.so.1.68.0 7f04a5d18000-7f04a5d19000 r--p 00019000 08:01 4346755 /usr/lib/libboost_filesystem.so.1.68.0 7f04a5d19000-7f04a5d1a000 rw-p 0001a000 08:01 4346755 /usr/lib/libboost_filesystem.so.1.68.0 7f04a5d1f000-7f04a5d9a000 r-xp 00000000 08:01 4346783 /usr/lib/libboost_program_options.so.1.68.0 7f04a5d9a000-7f04a5f99000 ---p 0007b000 08:01 4346783 /usr/lib/libboost_program_options.so.1.68.0 7f04a5f99000-7f04a5f9c000 r--p 0007a000 08:01 4346783 /usr/lib/libboost_program_options.so.1.68.0 7f04a5f9c000-7f04a5f9d000 rw-p 0007d000 08:01 4346783 /usr/lib/libboost_program_options.so.1.68.0 7f04a5f9f000-7f04a604f000 r-xp 00000000 08:01 4458257 /usr/local/lib/libhts.so.1.9 7f04a604f000-7f04a624e000 ---p 000b0000 08:01 4458257 /usr/local/lib/libhts.so.1.9 7f04a624e000-7f04a624f000 r--p 000af000 08:01 4458257 /usr/local/lib/libhts.so.1.9 7f04a624f000-7f04a6251000 rw-p 000b0000 08:01 4458257 /usr/local/lib/libhts.so.1.9 7f04a6257000-7f04a627d000 r-xp 00000000 08:01 2883642 /lib/x86_64-linux-gnu/ld-2.23.so 7f04a6478000-7f04a647c000 rw-p 00000000 00:00 0 7f04a647c000-7f04a647d000 r--p 00025000 08:01 2883642 /lib/x86_64-linux-gnu/ld-2.23.so 7f04a647d000-7f04a647e000 rw-p 00026000 08:01 2883642 /lib/x86_64-linux-gnu/ld-2.23.so 7f04a647e000-7f04a6480000 rw-p 00000000 00:00 0 7f04a6480000-7f04a6486000 rw-p 00000000 00:00 0 7ffe94737000-7ffe94773000 rw-p 00000000 00:00 0 [stack] 7ffe9478f000-7ffe94792000 r--p 00000000 00:00 0 [vvar] 7ffe94792000-7ffe94794000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)

DataOmics76 commented 5 years ago

I got it to work like the other user @vgastaldi told ^^

Now I will be waiting for the results!

Thanks!

cmake -DCMAKE_INSTALL_PREFIX="${HOME}/dng" -DCMAKE_BUILD_TYPE=Debug .. make -j4 make install

DataOmics76 commented 5 years ago

but I got...something weird on the results I asume

Created SNP lookup table First mrate: 1 last: 1 First code: 6 last: 6 First target string: AA/AA/AA last: TT/TT/TT First tref: 0.0002388 last: 0.99301

Created indel lookup table First code: 6 last: 6 First target string: RR/RR/RR last: DD/DD/DD First prior: 0.05 last: 0.114

Created paired lookup table First target string: AA/AA last: TT/TT First prior 1 last: 1

Total number of SNP sites interrogated: 0 Total number of SNP sites passing read-depth filters: 0 Total number of INDEL sites interrogated: 0 Total number of INDEL sites passing read-depth filters: 0 Total number of Paired sample sites interrogated: 0 Total number of Paired sample sites passing read-depth filters: 0 Done !

BCF PARSING ERROR - Unable to find trio! Members missing: 3! Skipping site10167

DataOmics76 commented 5 years ago

I found out reason here:

https://sourceforge.net/p/denovogear/discussion/h/thread/5814ad37/

saliksyed commented 5 years ago

I ran into this as well FYI


so.1.58.0
7f68e6544000-7f68e6545000 r--p 00002000 08:01 107207                     /usr/lib/x86_64-linux-gnu/libboost_system.
so.1.58.0
7f68e6545000-7f68e6546000 rw-p 00003000 08:01 107207                     /usr/lib/x86_64-linux-gnu/libboost_system.
so.1.58.0
7f68e6546000-7f68e655d000 r-xp 00000000 08:01 107349                     /usr/lib/x86_64-linux-gnu/libboost_filesys
tem.so.1.58.0
7f68e655d000-7f68e675c000 ---p 00017000 08:01 107349                     /usr/lib/x86_64-linux-gnu/libboost_filesys
tem.so.1.58.0
7f68e675c000-7f68e675d000 r--p 00016000 08:01 107349                     /usr/lib/x86_64-linux-gnu/libboost_filesys
tem.so.1.58.0
7f68e675d000-7f68e675e000 rw-p 00017000 08:01 107349                     /usr/lib/x86_64-linux-gnu/libboost_filesys
tem.so.1.58.0
7f68e675e000-7f68e67d8000 r-xp 00000000 08:01 107915                     /usr/lib/x86_64-linux-gnu/libboost_program
_options.so.1.58.0
7f68e67d8000-7f68e69d8000 ---p 0007a000 08:01 107915                     /usr/lib/x86_64-linux-gnu/libboost_program
_options.so.1.58.0
7f68e69d8000-7f68e69db000 r--p 0007a000 08:01 107915                     /usr/lib/x86_64-linux-gnu/libboost_program
_options.so.1.58.0
7f68e69db000-7f68e69dc000 rw-p 0007d000 08:01 107915                     /usr/lib/x86_64-linux-gnu/libboost_program
_options.so.1.58.0
7f68e69dc000-7f68e6a8a000 r-xp 00000000 08:01 92291                      /usr/local/lib/libhts.so.1.9
7f68e6a8a000-7f68e6c89000 ---p 000ae000 08:01 92291                      /usr/local/lib/libhts.so.1.9
7f68e6c89000-7f68e6c8a000 r--p 000ad000 08:01 92291                      /usr/local/lib/libhts.so.1.9
7f68e6c8a000-7f68e6c8c000 rw-p 000ae000 08:01 92291                      /usr/local/lib/libhts.so.1.9
7f68e6c8c000-7f68e6cb2000 r-xp 00000000 08:01 2000                       /lib/x86_64-linux-gnu/ld-2.23.so
7f68e6e9b000-7f68e6ea4000 rw-p 00000000 00:00 0 
7f68e6eaf000-7f68e6eb1000 rw-p 00000000 00:00 0 
7f68e6eb1000-7f68e6eb2000 r--p 00025000 08:01 2000                       /lib/x86_64-linux-gnu/ld-2.23.so
7f68e6eb2000-7f68e6eb3000 rw-p 00026000 08:01 2000                       /lib/x86_64-linux-gnu/ld-2.23.so
7f68e6eb3000-7f68e6eb4000 rw-p 00000000 00:00 0 
7ffc1f5d8000-7ffc1f615000 rw-p 00000000 00:00 0                          [stack]
7ffc1f72f000-7ffc1f732000 r--p 00000000 00:00 0                          [vvar]
7ffc1f732000-7ffc1f734000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)
saliksyed88@instance-1:~$ ```