vg view terminates

[MichelMoser]

Hi,

I am new to vg and just created my first GAM file, yeah =) Trying to view the GAM file on a Centos cluster with vg unfortunately failed. Downloaded the pre-build binaries and hit vg view alns.gam

Terminated with:

$ ~/tools/vg view alns.gam
terminate called after throwing an instance of 'std::runtime_error'
  what():  [stream::ProtobufIterator] could not parse message
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_SbEhoz/stacktrace.txt

Loos like there is some issue with Protobuf?

Stacktrace shows me:

Crash report for vg v1.14.0 "Quadrelle"
Stack trace (most recent call last):
#16   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x4cfcb9, in _start
#15   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18e54d8, in __libc_start_main
#14   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x407395, in main
#13   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x971c07, in vg::subcommand::Subcommand::operator()(int, char**) const
#12   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x982a1a, in main_view(int, char**)
#11   Object "/net/fs-1/home01/michelmo/tools/vg", at 0xa8897c, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#10   Object "/net/fs-1/home01/michelmo/tools/vg", at 0x97eac0, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#6}>::_M_invoke(std::_Any_data const&, std::istream&)
#9    Object "/net/fs-1/home01/michelmo/tools/vg", at 0xc6d6c3, in vg::VG::VG(std::istream&, bool, bool)
#8    Object "/net/fs-1/home01/michelmo/tools/vg", at 0xc6d14d, in vg::VG::from_istream(std::istream&, bool, bool)
#7    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x6bcf8d, in void vg::stream::for_each<vg::Graph>(std::istream&, std::function<void (long, vg::Graph&)> const&)
#6    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x6bceb4, in vg::stream::ProtobufIterator<vg::Graph>::fill_value()
#5    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f463, in __cxa_throw
#4    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f910, in std::terminate()
#3    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f8c5, in __cxxabiv1::__terminate(void (*)())
#2    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18c1c44, in __gnu_cxx::__verbose_terminate_handler()
#1    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18f5d40, in abort
#0    Object "/net/fs-1/home01/michelmo/tools/vg", at 0x1020267, in raise

Any help or ideas would be appreciated.
Thank you,
Michel

[ekg]

Although there are efforts to fix this, for the moment you need to tell vg view that you are giving it alignments using `vg view -a ...`

…

On Fri, Apr 5, 2019, 12:53 MichelMoser ***@***.***> wrote: Hi, I am new to vg and just created my first GAM file, yeah =) Trying to view the GAM file on a Centos cluster with vg unfortunately failed. Downloaded the pre-build binaries and hit vg view alns.gam Terminated with: $ ~/tools/vg view alns.gam terminate called after throwing an instance of 'std::runtime_error' what(): [stream::ProtobufIterator] could not parse message ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_SbEhoz/stacktrace.txt Loos like there is some issue with Protobuf? Stacktrace shows me: Crash report for vg v1.14.0 "Quadrelle" Stack trace (most recent call last): #16 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x4cfcb9, in _start #15 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18e54d8, in __libc_start_main #14 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x407395, in main #13 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x971c07, in vg::subcommand::Subcommand::operator()(int, char**) const #12 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x982a1a, in main_view(int, char**) #11 Object "/net/fs-1/home01/michelmo/tools/vg", at 0xa8897c, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>) #10 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x97eac0, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#6}>::_M_invoke(std::_Any_data const&, std::istream&) #9 Object "/net/fs-1/home01/michelmo/tools/vg", at 0xc6d6c3, in vg::VG::VG(std::istream&, bool, bool) #8 Object "/net/fs-1/home01/michelmo/tools/vg", at 0xc6d14d, in vg::VG::from_istream(std::istream&, bool, bool) #7 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x6bcf8d, in void vg::stream::for_each<vg::Graph>(std::istream&, std::function<void (long, vg::Graph&)> const&) #6 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x6bceb4, in vg::stream::ProtobufIterator<vg::Graph>::fill_value() #5 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f463, in __cxa_throw #4 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f910, in std::terminate() #3 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x182f8c5, in __cxxabiv1::__terminate(void (*)()) #2 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18c1c44, in __gnu_cxx::__verbose_terminate_handler() #1 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x18f5d40, in abort #0 Object "/net/fs-1/home01/michelmo/tools/vg", at 0x1020267, in raise ``` Any help or ideas would be appreciated. Thank you, Michel — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2196>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI4EchRJGqipS3o0ZvNMYEXE5ZvUerQks5vdytHgaJpZM4ceqks> .

[MichelMoser]

Thanks