Error When Running "vg gbwt --gbz-format -g hprc-v1.0-mc-grch38.gfa.gz -G hprc-v1.0-mc-grch38.gfa"

[AbdelF6]

1. What were you trying to do?
Trying to run the vg gbwt command

2. What did you want to happen?
Command to provide

3. What actually happened?
Terminal Output:

terminate called after throwing an instance of 'std::runtime_error'
  what():  GFAFile: Invalid walk segment > on line 6079839
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.59.0-24-g4db75c210 "Casatico"
Stack trace (most recent call last):
#16   Object "", at 0xffffffffffffffff, in
#15   Object "/home/houlahanlab/vg/bin/vg", at 0x558ecad7a194, in _start
#14   Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fdd8a1f8e3f, in __libc_start_main
#13   Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fdd8a1f8d8f, in
#12   Object "/home/houlahanlab/vg/bin/vg", at 0x558ecb56f0ab, in vg::subcommand::Subcommand::operator()(int, char**) const
    | Source "src/subcommand/subcommand.cpp", line 75, in operator()
      Source "/usr/include/c++/11/bits/std_function.h", line 590, in operator() [0x558ecb56f0ab]
        587:       {
        588:    if (_M_empty())
        589:      __throw_bad_function_call();
      > 590:    return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
        591:       }
        592:
        593: #if __cpp_rtti
#11   Object "/home/houlahanlab/vg/bin/vg", at 0x558ecb47d4cd, in main_gbwt(int, char**)
      Source "src/subcommand/gbwt_main.cpp", line 188, in main_gbwt [0x558ecb47d4cd]
#10   Object "/home/houlahanlab/vg/bin/vg", at 0x558ecb47b2b7, in step_1_build_gbwts(vg::GBWTHandler&, GraphHandler&, GBWTConfig&)
      Source "src/subcommand/gbwt_main.cpp", line 1347, in step_1_build_gbwts [0x558ecb47b2b7]
#9    Object "/home/houlahanlab/vg/bin/vg", at 0x558ecbe2a826, in gbwtgraph::gfa_to_gbwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, gbwtgraph::GFAParsingParameters const&)
      Source "src/gfa.cpp", line 1246, in gfa_to_gbwt [0x558ecbe2a826]
#8    Object "/home/houlahanlab/vg/bin/vg", at 0x558ecbe25912, in gbwtgraph::GFAFile::GFAFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)
      Source "src/gfa.cpp", line 380, in GFAFile [0x558ecbe25912]
#7    Object "/home/houlahanlab/vg/bin/vg", at 0x558ecad09484, in gbwtgraph::GFAFile::add_w_line(char const*, unsigned long) [clone .cold]
      Source "src/gfa.cpp", line 579, in add_w_line [0x558ecad09484]
#6    Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7fdd8a5124d7, in __cxa_throw
#5    Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7fdd8a512276, in std::terminate()
#4    Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7fdd8a51220b, in
#3    Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30", at 0x7fdd8a506b9d, in
#2    Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fdd8a1f77f2, in abort
#1    Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fdd8a211475, in raise
#0    Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fdd8a2659fc, in pthread_kill

5. What data and command can the vg dev team use to make the problem happen?
vg gbwt with the pangenome data

6. What does running vg version say?

vg version v1.59.0-24-g4db75c210 "Casatico"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528

[jltsiren]

The GFA file is likely corrupted. The error message indicates that on (0-based) line 6079839, there is a > followed by one of \n, \t, >, <, or EOF in the walk field.