vg index crashes

[bcantarel]

Hi was running through the mini graph-cactus SOP and afterwards I ran vg index to create the xg index file that can be used for mapping -- I tried this with a small set of sequence (2) and it worked great but with a larger set (16) I am getting the following crash report
vg index -t 64 -x out.xg -g out.gcsa out.vg

vg: /private/home/anovak/workspace2/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 v1.50.1 "Monopoli"
Stack trace (most recent call last):
#13 Object "/home/cactus/bin/vg", at 0x6163d4, in _start
#12 Object "/home/cactus/bin/vg", at 0x205e5f6, in __libc_start_main
#11 Object "/home/cactus/bin/vg", at 0x205cd99, in __libc_start_call_main
#10 Object "/home/cactus/bin/vg", at 0xdf5fab, in vg::subcommand::Subcommand::operator()(int, char**) const
#9 Object "/home/cactus/bin/vg", at 0xd67534, in main_index(int, char**)
#8 Object "/home/cactus/bin/vg", at 0x14ab69e, in vg::VGset::to_xg(xg::XG&, std::function<bool (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&, std::map<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, vg::Path, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, vg::Path> > >*)
#7 Object "/home/cactus/bin/vg", at 0x188b3ca, in xg::XG::from_enumerators(std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > 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, std::allocator > const&, long long const&, bool const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, bool const&, bool const&)> const&)> const&, bool, std::__cxx11::basic_string<char, std::char_traits, std::allocator >)
#6 Object "/home/cactus/bin/vg", at 0x1884337, in xg::XG::index_node_to_path(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)
#5 Object "/home/cactus/bin/vg", at 0x188c7eb, in sdsl::int_vector<(unsigned char)0>::operator[](unsigned long const&) const
#4 Object "/home/cactus/bin/vg", at 0x206f1c5, in __assert_fail
#3 Object "/home/cactus/bin/vg", at 0x5e5053, in __assert_fail_base.cold
#2 Object "/home/cactus/bin/vg", at 0x5e512b, in abort
#1 Object "/home/cactus/bin/vg", at 0x20757d5, in raise
#0 Object "/home/cactus/bin/vg", at 0x20a21dc, 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!`

[jeizenga]

Are you able to share the inputs that led to this crash?

[bcantarel]

Sure -- since it's very large, here is a link https://storage.googleapis.com/bioinfo-workflow-references/pangenomeTestingData/out.vg and https://storage.googleapis.com/bioinfo-workflow-references/pangenomeTestingData/out.snarls.txt

[jeizenga]

Thanks for providing the data. I have not been able to reproduce the crash so far. Could you check the VG version you are using? This could be a bug that has already been fixed. You could also try to reproduce the crash yourself using the inputs you gave me. That could help establish if the crash is non-deterministic or if it's some kind of interaction with your server environment.

[bcantarel]

Ok thanks! I will try with the version released 2 weeks ago.

[jeizenga]

I'm going to close this issue since we haven't heard any more news. Let me know if this is not correct.