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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg id command showing error #3848

Open Zer0day-0 opened 1 year ago

Zer0day-0 commented 1 year ago

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
Ahahaha3 commented 9 months ago

Do you have resolve the problem? and what's the size of your reference genome?