vg genotype crash during vcf recall

[bvalot]

Please describe:

1. What you were trying to do Try to obtained a vcf file with a recall from alignment
2. What you wanted to happen Obtained an vcf with genotype information
3. What actually happened The program crash
4. What data and command line to use to make the problem recur, if applicable

   
   participant@t7:~/data/bacteria/work$  vg genotype -v -G gyrA_full.gam -V gyrA_full.vcf gyrA_full.vg
   vg: src/path_index.cpp:254: vg::PathIndex::PathIndex(vg::VG&, const string&, bool): Assertion `vg.paths.has_path(path_name)' failed.
   ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
   Stack trace path: /tmp/vg_crash_nb7Wux/stacktrace.txt

participant@t7:~/data/bacteria/work$ cat /tmp/vg_crash_nb7Wux/stacktrace.txt Stack trace (most recent call last):

13 Object "/usr/local/bin/vg", at 0x4b9c78, in _start

12 Object "/usr/local/bin/vg", at 0x114ed29, in __libc_start_main

11 Object "/usr/local/bin/vg", at 0x114eb35, in generic_start_main

10 Object "/usr/local/bin/vg", at 0x404eb6, in main

  Source "src/main.cpp", line 61, in main [0x404eb6]

9 Object "/usr/local/bin/vg", at 0x7e3827, in vg::subcommand::Subcommand::operator()(int, char**) const

| Source "src/subcommand/subcommand.cpp", line 72, in operator()
  Source "/usr/include/c++/5/functional", line 2267, in operator() [0x7e3827]
   2264:     {
   2265:       if (_M_empty())
   2266:    __throw_bad_function_call();
  >2267:       return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
   2268:     }
   2269: 
   2270: #if __cpp_rtti

8 Object "/usr/local/bin/vg", at 0x7a457c, in main_genotype(int, char**)

  Source "src/subcommand/genotype_main.cpp", line 401, in main_genotype [0x7a457c]

7 Object "/usr/local/bin/vg", at 0x981b78, in vg::Genotyper::run(vg::AugmentedGraph&, std::ostream&, std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, bool, bool, bool, int, int)

  Source "src/genotyper.cpp", line 124, in run [0x981b78]

6 Object "/usr/local/bin/vg", at 0xa97852, in vg::PathIndex::PathIndex(vg::VG&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, bool)

  Source "src/path_index.cpp", line 254, in PathIndex [0xa97852]

5 Object "/usr/local/bin/vg", at 0x11526ad, in __assert_fail

4 Object "/usr/local/bin/vg", at 0x115264a, in __assert_fail_base

3 Object "/usr/local/bin/vg", at 0x115f449, in abort

2 Object "/usr/local/bin/vg", at 0xce43e9, in raise

  Source "../sysdeps/unix/sysv/linux/pt-raise.c", line 35, in raise [0xce43e9]

1 Object "/usr/local/bin/vg", at 0xce441f, in

0 Object "/usr/local/bin/vg", at 0x879fd7, in vg::emit_stacktrace(int, siginfo_t, void)

  Source "src/crash.cpp", line 170, in emit_stacktrace [0x879fd7]

[edawson]

Hi @bvalot ,

The "recall" functionality of vg was an early experiment at genotyping structural variants. It has very specific required inputs. Can you provide your command lines for constructing and indexing the graph?

Does your graph contain only SNVs/indels or does it contain structural variants?

I would direct you to the call command if you'd like to call variants and genotype them. I'm happy to help debug the recall pipeline but my guess is vg call will accomplish what you want.

Out of curiosity - how did you stumble upon recall? As the docs are out of date I'd like to update the source that directed you to try it.