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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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VG has crashed when run vg msga #3288

Open kangxiongbin opened 3 years ago

kangxiongbin commented 3 years ago

1. What were you trying to do? I try to bulid a VG. My data is 526K including 810 contigs.

2. What did you want to happen? provide me a graph

3. What actually happened? crashed

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:

/tmp/vg_crash_lyUUyV/stacktrace.txt：

Crash report for vg v1.32.0 "Sedlo"
Stack trace (most recent call last):
#12   Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x59fe8d, in _start
#11   Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x1d6d9df, in __libc_start_main
#10   Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x578414, in main
#9    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0xb7b91b, in vg::subcommand::Subcommand::operator()(int, char**) const
#8    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0xb4db4b, in main_msga(int, char**)
#7    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x116cef4, in vg::algorithms::path_string[abi:cxx11](handlegraph::HandleGraph const&, vg::Path const&)
#6    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x4fbac1, in vg::VG::get_sequence[abi:cxx11](handlegraph::handle_t const&) const [clone .cold]
#5    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x1ca97e8, in __cxa_throw
#4    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x1ca9686, in std::terminate()
#3    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x1ca961b, in __cxxabiv1::__terminate(void (*)())
#2    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x574ec2, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x577953, in abort
#0    Object "/prj/metastrain/software/conda/envs/py3/bin/vg", at 0x127feeb, in raise

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

6. What does running vg version say?

vg v1.32.0
glennhickey commented 3 years ago

Sorry, we're no longer supporting msga:

vg msga

WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely.

!!!
WARNING
!!!
vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups.

usage: vg msga [options] >graph.vg
adamnovak commented 3 years ago

The best replacement for msga is I think pggb which can do a similar operation.