VG crashed making xg from vg on HPRC v2 graph

[daanishmahajan]

1. What were you trying to do?
I was running VG snarls on the HPRC v2 CHM13 graph. System specifications:

Dual-socket Intel Xeon Gold 6248R server with 2 X 24 cores and 750 GB RAM.

2. What happened?
VG crashed.

3. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

vg: /public/home/anovak/build/vg/include/sdsl/int_vector.hpp:1436: sdsl::int_vector<<anonymous> >::const_reference sdsl::int_vector<<anonymous> >::operator[](const size_type&) const [with unsigned char t_width = 0; sdsl::int_vector<<anonymous> >::const_reference = long unsigned int; sdsl::int_vector<<anonymous> >::size_type = long unsigned int]: Assertion `idx < this->size()' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.61.0 "Plodio"
Stack trace (most recent call last):
#13   Object "/home/daanish/bin/vg", at 0x623c34, in _start
#12   Object "/home/daanish/bin/vg", at 0x20e46d6, in __libc_start_main
#11   Object "/home/daanish/bin/vg", at 0x20e2e39, in __libc_start_call_main
#10   Object "/home/daanish/bin/vg", at 0xe1721b, in vg::subcommand::Subcommand::operator()(int, char**) const
#9    Object "/home/daanish/bin/vg", at 0xd87ecc, in main_index(int, char**)
#8    Object "/home/daanish/bin/vg", at 0x14f5ade, in vg::VGset::to_xg(xg::XG&, std::function<bool (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, vg::Path, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, vg::Path> > >*)
#7    Object "/home/daanish/bin/vg", at 0x18b76f2, in xg::XG::from_enumerators(std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long long const&)> const&)> const&, std::function<void (std::function<void (long long const&, bool const&, long long const&, bool const&)> const&)> const&, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, long long const&, bool const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool const&, bool const&)> const&)> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
#6    Object "/home/daanish/bin/vg", at 0x18b0744, in xg::XG::index_node_to_path(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
#5    Object "/home/daanish/bin/vg", at 0x1850c1b, in sdsl::int_vector<(unsigned char)0>::operator[](unsigned long const&) const
#4    Object "/home/daanish/bin/vg", at 0x20f52a5, in __assert_fail
#3    Object "/home/daanish/bin/vg", at 0x5f26db, in __assert_fail_base.cold
#2    Object "/home/daanish/bin/vg", at 0x5f27b3, in abort
#1    Object "/home/daanish/bin/vg", at 0x20fb8b5, in raise
#0    Object "/home/daanish/bin/vg", at 0x212840c, in __pthread_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!

4. What data and command can the vg dev team use to make the problem happen?
Data -

s3://human-pangenomics/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.gfa.gz

Command -

vg convert -g <INPUT\_FILE\_PATH> > FILE.vg
vg index -x FILE.xg FILE.vg
vg snarls -t 48 FILE.xg > <OUTPUT\_FILE\_PATH>

6. What does running vg version say?

v1.61.0

[adamnovak]

I don't see a reason why what you're trying to do shouldn't work, so this definitely seems like a bug. It looks like it is failing at the step of making the .xg file.

As a workaround, you can go directly from GFA to XG with one vg convert command:

vg convert -g <INPUT\_FILE\_PATH> --xg-out > FILE.vg

If your GFA is well-behaved and uses numerical node IDs (like the one you link ought to be), you could also I think pass it directly to vg snarls.

[daanishmahajan]

Thanks, it worked.

[adamnovak]

I'm going to reopen this because I'm still trying to reproduce the original crash.