genotyper: cactus source sink looks for node 0

[ekg]

In vg genotype it looks like the cactus source sink node finding is failing.

To reproduce:

wget http://hypervolu.me/~erik/vg/cactus0.tar.gz
tar xzvf cactus0.tar.gz
gdb vg -ex 'r genotype primary-graph.chopped.vg NA12878.illumina_downsampled.gam.index -C >/tmp/NA12878.illumina.loci.1'

This will fail:

(gdb) bt
#0  0x0000000000b8f0e5 in raise ()
#1  0x0000000000b0a65b in abort ()
#2  0x0000000000ad4c6d in __gnu_cxx::__verbose_terminate_handler() ()
    at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/vterminate.cc:95
#3  0x0000000000a83ad6 in __cxxabiv1::__terminate(void (*)()) ()
    at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:47
#4  0x0000000000a83b21 in std::terminate() ()
    at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:57
#5  0x0000000000a83c28 in __cxa_throw ()
    at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_throw.cc:87
#6  0x00000000004bb251 in vg::VG::get_node(long) () at src/vg.cpp:4491
#7  0x00000000004bf1fd in vg::VG::is_tail_node(long) () at src/vg.cpp:9027
#8  0x00000000005f6b01 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int)::{lambda(long)#1}::
operator()(long) const () at src/bubbles.cpp:286
#9  0x00000000005f6c5c in std::_Function_handler<std::pair<long, long> (long), vg::get_cactus_source_sink(
vg::VG&, std::string const&, int)::{lambda(long)#1}>::_M_invoke(std::_Any_data const&, long) ()
    at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2025
#10 0x00000000005f7331 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int) ()
    at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2439
#11 0x00000000005b9d9c in vg::Genotyper::find_sites_with_cactus(vg::VG&, std::string const&) ()
    at src/genotyper.cpp:714
#12 0x00000000005c2274 in vg::Genotyper::run(vg::VG&, std::vector<vg::Alignment, std::allocator<vg::Alignm
ent> >&, std::ostream&, std::string, std::string, std::string, std::string, bool, bool, bool, bool, bool, 
int, int) () at src/genotyper.cpp:251
#13 0x0000000000445ff9 in main_genotype(int, char**) () at src/main.cpp:1823
#14 0x0000000000408882 in main () at src/main.cpp:8913

[glennhickey]

That was fixed in vg master via PR #521.

On Thu, Nov 10, 2016 at 11:15 AM, Erik Garrison notifications@github.com
wrote:

In vg genotype it looks like the cactus source sink node finding is
failing.

To reproduce:

wget http://hypervolu.me/~erik/vg/cactus0.tar.gz
tar xzvf cactus0.tar.gz
gdb vg -ex 'r genotype primary-graph.chopped.vg NA12878.illumina_downsampled.gam.index -C >/tmp/NA12878.illumina.loci.1'

This will fail:

(gdb) bt
#0 0x0000000000b8f0e5 in raise ()
#1 0x0000000000b0a65b in abort ()
#2 0x0000000000ad4c6d in __gnu_cxx::__verbose_terminate_handler() ()
at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/vterminate.cc:95
#3 0x0000000000a83ad6 in __cxxabiv1::__terminate(void (_)()) ()
at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:47
#4 0x0000000000a83b21 in std::terminate() ()
at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:57
#5 0x0000000000a83c28 in __cxa_throw ()
at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_throw.cc:87
#6 0x00000000004bb251 in vg::VG::get_node(long) () at src/vg.cpp:4491
#7 0x00000000004bf1fd in vg::VG::is_tail_node(long) () at src/vg.cpp:9027
#8 0x00000000005f6b01 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int)::{lambda(long)#1}::
operator()(long) const () at src/bubbles.cpp:286
#9 0x00000000005f6c5c in std::_Function_handler<std::pair<long, long> (long), vg::get_cactus_source_sink(
vg::VG&, std::string const&, int)::{lambda(long)#1}>::_M_invoke(std::Any_data const&, long) ()
at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2025
#10 0x00000000005f7331 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int) ()
at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2439
#11 0x00000000005b9d9c in vg::Genotyper::find_sites_with_cactus(vg::VG&, std::string const&) ()
at src/genotyper.cpp:714
#12 0x00000000005c2274 in vg::Genotyper::run(vg::VG&, std::vector<vg::Alignment, std::allocator<vg::Alignm
ent> >&, std::ostream&, std::string, std::string, std::string, std::string, bool, bool, bool, bool, bool,
int, int) () at src/genotyper.cpp:251
#13 0x0000000000445ff9 in main_genotype(int, char*) () at src/main.cpp:1823
#14 0x0000000000408882 in main () at src/main.cpp:8913

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[shilpagarg]

After following steps at PR #521: I get
terminate called after throwing an instance of 'std::runtime_error'
what(): No node 925833952 in graph
Aborted

and here is the bt:

#0  0x0000000000bbaf15 in raise ()
#1  0x0000000000b3648b in abort ()
#2  0x0000000000b00a9d in __gnu_cxx::__verbose_terminate_handler() () at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/vterminate.cc:95
#3  0x0000000000aaf906 in __cxxabiv1::__terminate(void (*)()) () at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:47
#4  0x0000000000aaf951 in std::terminate() () at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:57
#5  0x0000000000aafa58 in __cxa_throw () at /lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_throw.cc:87
#6  0x00000000004c11b1 in vg::VG::get_node(long) () at src/vg.cpp:4572
#7  0x00000000004c4e2d in vg::VG::is_tail_node(long) () at src/vg.cpp:9041
#8  0x0000000000600a71 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int)::{lambda(long)#1}::operator()(long) const () at src/bubbles.cpp:286
#9  0x0000000000600bcc in std::_Function_handler<std::pair<long, long> (long), vg::get_cactus_source_sink(vg::VG&, std::string const&, int)::{lambda(long)#1}>::_M_invoke(std::_Any_data const&, long) () at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2025
#10 0x00000000006012a1 in vg::get_cactus_source_sink(vg::VG&, std::string const&, int) () at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2439
#11 0x00000000005c2fcc in vg::Genotyper::find_sites_with_cactus(vg::VG&, std::string const&) () at src/genotyper.cpp:714
#12 0x00000000005cb4a4 in vg::Genotyper::run(vg::VG&, std::vector<vg::Alignment, std::allocator<vg::Alignment> >&, std::ostream&, std::string, std::string, std::string, std::string, bool, bool, bool, bool, bool, int, int) () at src/genotyper.cpp:251
#13 0x00000000004466d9 in main_genotype(int, char**) () at src/main.cpp:1834
#14 0x0000000000408852 in main () at src/main.cpp:9335

[glennhickey]

#8 in your stack trace refers to a function *vg::get_cactus_source_sink *that
was removed in the PR in question. In this commit:

67e8b2c

If you update your vg this should go away.

On Thu, Nov 10, 2016 at 4:13 PM, shilpagarg notifications@github.com
wrote:

After following steps at PR #521 #521:
I get
terminate called after throwing an instance of 'std::runtime_error'
what(): No node 925833952 in graph
Aborted

and here is the bt:
#0 0x0000000000bbaf15 in raise ()
#1 #1 0x0000000000b3648b in abort ()
#2 #2 0x0000000000b00a9d in
__gnu_cxx::__verbose_terminate_handler() () at
/lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/
libstdc++-v3/libsupc++/vterminate.cc:95
#3 #3 0x0000000000aaf906 in
__cxxabiv1::__terminate(void (

_)()) () at
/lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:47
#4 #4 0x0000000000aaf951 in
std::terminate() () at
/lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_terminate.cc:57
#5 #5 0x0000000000aafa58 in
__cxa_throw () at
/lustre/scratch110/sanger/gt1/build/gcc/gcc-4.9.2-src/libstdc++-v3/libsupc++/eh_throw.cc:87
#6 #6 0x00000000004c11b1 in
vg::VG::get_node(long) () at src/vg.cpp:4572 #7
#7 0x00000000004c4e2d in
vg::VG::is_tail_node(long) () at src/vg.cpp:9041 #8
#8 0x0000000000600a71 in
vg::get_cactus_source_sink(vg::VG&, std::string const&,
int)::{lambda(long)#1
https://github.com/vgteam/vg/issues/1}::operator()(long) const () at
src/bubbles.cpp:286 #9 #9
0x0000000000600bcc in std::Function_handler (long),
vg::get_cactus_source_sink(vg::VG&, std::string const&,
int)::{lambda(long)#1
https://github.com/vgteam/vg/issues/1}>::_M_invoke(std::_Any_data const&,
long) () at /software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2025 #10
#10 0x00000000006012a1 in
vg::get_cactus_source_sink(vg::VG&, std::string const&, int) () at
/software/hpag/gcc/4.9.2/include/c++/4.9.2/functional:2439 #11
#11 0x00000000005c2fcc in
vg::Genotyper::find_sites_with_cactus(vg::VG&, std::string const&) () at
src/genotyper.cpp:714 #12 #12
0x00000000005cb4a4 in vg::Genotyper::run(vg::VG&, std::vector >&,
std::ostream&, std::string, std::string, std::string, std::string, bool,
bool, bool, bool, bool, int, int) () at src/genotyper.cpp:251 #13
#13 0x00000000004466d9 in
main_genotype(int, char*) () at src/main.cpp:1834
#14 #14 0x0000000000408852 in main
() at src/main.cpp:9335

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[adamnovak]

I'm going to assume Glenn's advice worked.