1. What were you trying to do?
I am trying to generate vg node IDs using the vg id command. I am using the .vg files generated by using vg construct in this link.
2. What did you want to happen?
I wanted to generate a joint id space across each graph using the already constructed .vg files.
3. What actually happened?
vg crashed with showing the following error.
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
terminate called after throwing an instance of 'std::runtime_error'
what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 5942229575493 group 5942229575489
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_Wk0wt4/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 v1.45.0 "Alpicella"
Stack trace (most recent call last):
#24 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x5e609d, in _start
#23 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x1e83eef, in __libc_start_main
#22 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x5b6a6e, in main
#21 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xcef6cb, in vg::subcommand::Subcommand::operator()(int, char**) const
#20 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xc6c99f, in main_ids(int, char**)
#19 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x12b3109, in vg::VGset::merge_id_space()
#18 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x12b2fa2, in vg::VGset::transform(std::function<void (handlegraph::MutableHandleGraph*)>)
#17 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xef2210, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#16 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x12b31eb, 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&)
#15 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x85cb0a, in vg::io::VPKG::with_putback(std::istream&, std::function<void (std::istream&)> const&)
#14 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xbeec5c, 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 "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xbf076f, 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 "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x13d282e, 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 const&, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&)> const&)
#11 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x138e058, 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 "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x138da8a, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (vg::Graph&)> const&)> const&)
#9 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x138b3b1, 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 "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0xbee9d4, 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 "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x1b6b2de, in vg::io::MessageIterator::operator++()
#6 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x5a1343, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold]
#5 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x1dbff68, in __cxa_throw
#4 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x1dbfe06, in std::terminate()
#3 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x1dbfd9b, in __cxxabiv1::__terminate(void (*)())
#2 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x5b35fa, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x5b5f97, in abort
#0 Object "/data/sata_data/home/dl8/anaconda3/envs/pangenome/bin/vg", at 0x144d17b, in raise
5. What data and command can the vg dev team use to make the problem happen?
vg ids -j $(for i in $(seq 1 22; echo X; echo Y); do echo $i.vg; done)
6. What does running vg version say?
vg version v1.45.0 "Alpicella"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux
Linked against libstd++ 20210601
Built by anovak@octagon
1. What were you trying to do? I am trying to generate vg node IDs using the vg id command. I am using the .vg files generated by using vg construct in this link.
2. What did you want to happen? I wanted to generate a joint id space across each graph using the already constructed .vg files.
3. What actually happened? vg crashed with showing the following error.
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:5. What data and command can the vg dev team use to make the problem happen?
vg ids -j $(for i in $(seq 1 22; echo X; echo Y); do echo $i.vg; done)
6. What does running
vg version
say?