The problem of vg ids

[Ahahaha3]

1. What were you trying to do?

vg ids -j Chr08.vg

2. What did you want to happen? run vg ids -j Chr08.vg

3. What actually happened? [E::bgzf_read_block] Failed to read BGZF block data at offset 223594034 expected 13261 bytes; hread returned 9119 terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 14589258281639 group 14589258281635 ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kUH8AU/stacktrace.txt Please include the stack trace file in your bug report!

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

Crash report for vg v1.38.0 "Canossa"
Stack trace (most recent call last):
#23   Object "/work/home/acttpa2z6s/software/vg", at 0x5b635d, in _start
#22   Object "/work/home/acttpa2z6s/software/vg", at 0x1cb357f, in __libc_start_main
#21   Object "/work/home/acttpa2z6s/software/vg", at 0x58a62e, in main
#20   Object "/work/home/acttpa2z6s/software/vg", at 0xbf999b, in vg::subcommand::Subcommand::operator()(int, char**) const
#19   Object "/work/home/acttpa2z6s/software/vg", at 0xb784df, in main_ids(int, char**)
#18   Object "/work/home/acttpa2z6s/software/vg", at 0x11e6209, in vg::VGset::merge_id_space()
#17   Object "/work/home/acttpa2z6s/software/vg", at 0x11e60a2, in vg::VGset::transform(std::function<void (handlegraph::MutableHandleGraph*)>)
#16   Object "/work/home/acttpa2z6s/software/vg", at 0xdcb260, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#15   Object "/work/home/acttpa2z6s/software/vg", at 0x11e62fe, in std::_Function_handler<void (std::istream&), vg::VGset::transform(std::function<void (handlegraph::MutableHandleGraph*)>)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#14   Object "/work/home/acttpa2z6s/software/vg", at 0xb5191c, in std::_Function_handler<void (std::istream&), vg::io::VPKG::try_load_one<handlegraph::MutablePathMutableHandleGraph>(std::istream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#13   Object "/work/home/acttpa2z6s/software/vg", at 0xb5342f, in std::_Function_handler<void (std::istream&), vg::io::VPKG::try_load_encapsulated<handlegraph::MutablePathMutableHandleGraph>(std::istream&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#12   Object "/work/home/acttpa2z6s/software/vg", at 0x12a6255, in std::_Function_handler<void* (std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)#3}>::_M_invoke(std::_Any_data har_traits<char>, std::allocator<char> > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::is
tream&)
#13   Object "/work/home/acttpa2z6s/software/vg", at 0xb5342f, in std::_Function_handler<void (std::istream&), vg::io:
:VPKG::try_load_encapsulated<handlegraph::MutablePathMutableHandleGraph>(std::istream&)::{lambda(std::istream&)#1}>::_
M_invoke(std::_Any_data const&, std::istream&)
#12   Object "/work/home/acttpa2z6s/software/vg", at 0x12a6255, in std::_Function_handler<void* (std::function<void (s
td::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> c
onst&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function<void (std::function<void (std::__cxx11::basi
c_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)#3}>::_M_invoke(std::_Any_data
const&, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)
#11   Object "/work/home/acttpa2z6s/software/vg", at 0x126ffd8, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)
#10   Object "/work/home/acttpa2z6s/software/vg", at 0x126fa0a, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (vg::Graph&)> const&)> const&)
#9    Object "/work/home/acttpa2z6s/software/vg", at 0x126d331, in std::_Function_handler<void (std::function<void (vg::Graph&)> const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)::{lambda(std::function<void (vg::Graph&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function<void (vg::Graph&)> const&)
#8    Object "/work/home/acttpa2z6s/software/vg", at 0xb51694, in std::_Function_handler<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&), vg::io::VPKG::try_load_encapsulated<handlegraph::MutablePathMutableHandleGraph>(vg::io::MessageIterator&)::{lambda(std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)
#7    Object "/work/home/acttpa2z6s/software/vg", at 0x12efa4a, in vg::io::MessageIterator::operator++()
#6    Object "/work/home/acttpa2z6s/software/vg", at 0x5430cd, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold]
#5    Object "/work/home/acttpa2z6s/software/vg", at 0x1bef608, in __cxa_throw
#4    Object "/work/home/acttpa2z6s/software/vg", at 0x1bef4a6, in std::terminate()
#3    Object "/work/home/acttpa2z6s/software/vg", at 0x1bef43b, in __cxxabiv1::__terminate(void (*)())
#2    Object "/work/home/acttpa2z6s/software/vg", at 0x5871ba, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1    Object "/work/home/acttpa2z6s/software/vg", at 0x589b53, in abort
#0    Object "/work/home/acttpa2z6s/software/vg", at 0x136b1cb, in raise

5. What data and command can the vg dev team use to make the problem happen? i used the vcf.gz file by syri

6. What does running vg version say?

vg version v1.38.0 "Canossa"
Compiled with g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 on Linux
Linked against libstd++ 20200808
Built by anovak@octagon