error [vg convert]: Input GFA is not acceptable.

moldach commented 3 years ago

What were you trying to do?**

I'm trying to convert a .gff file created by MoMI-G into a .vg file using vg but I get an error.

$ vg convert -g -p [ggf file] > output.vg
error [vg convert]: Input GFA is not acceptable.
error:[gfa_to_handle_graph] Found edge record with missing source name

Not sure why I get a GFA error when the input is GGF? The developer of MoMI-G thinks it's an underlying vg issue at this point.

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

Ultimately I could share some data with you if needed; however, the error is occuring on patient data so I would need to re-run using a public GIAB-trio first to see if I get the same error so it's a non-trivial issue.

What does running `vg version` say?**

$ vg version
vg version v1.28.0 "Acquafredda"
Compiled with g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 on Linux
Linked against libstd++ 20200808
Built by erik@beyyo

Additional

The link to the original issue is here (now a cross-tool issue?): https://github.com/MoMI-G/MoMI-G/issues/42

jeizenga commented 3 years ago

The vg convert -g command expects a GFA file, not a GFF file. Is that where the error is occurring? If in fact you are giving it a GFA file, then that error suggests that there is an L line that is malformed (specifically that it's missing the ID of an S line).

moldach commented 3 years ago

The author has updated the tool to create .gfa file.

What do you make of the following error?

$ vg convert -g -p momig-vcf-test-output.gfa > output.vg
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion `false' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_uw0zv2/stacktrace.txt
Please include the stack trace file in your bug report!

  1 Crash report for vg v1.28.0 "Acquafredda"
      2 Stack trace (most recent call last):
      3 #12   Object "/home/mtg/bin/vg", at 0x661d0d, in _start
      4 #11   Object "/home/mtg/bin/vg", at 0x1f49d1f, in __libc_start_main
      5 #10   Object "/home/mtg/bin/vg", at 0x57f838, in main
      6 #9    Object "/home/mtg/bin/vg", at 0xc3523b, in vg::subcommand::Subcommand::operator()(int, char**) const
      7 #8    Object "/home/mtg/bin/vg", at 0xcad624, in main_convert(int, char**)
      8 #7    Object "/home/mtg/bin/vg", at 0x118f2e5, in vg::algorithms::gfa_to_path_handle_graph(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, handlegraph::MutableHandleGraph*, bool, bool)
      9 #6    Object "/home/mtg/bin/vg", at 0x118e720, in vg::algorithms::gfa_to_handle_graph_on_disk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, handlegraph:MutableHandleGraph*, bool, gfak::GFAKluge&)
     10 #5    Object "/home/mtg/bin/vg", at 0x119370b, in gfak::GFAKluge::for_each_sequence_line_in_file(char const*, std::function<void (gfak::sequence_elem const&)>)
     11 #4    Object "/home/mtg/bin/vg", at 0x118fbc5, in gfak::mmap_open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, int&)
     12 #3    Object "/home/mtg/bin/vg", at 0x1f59ff5, in __assert_fail
     13 #2    Object "/home/mtg/bin/vg", at 0x57ec63, in __assert_fail_base.cold
     14 #1    Object "/home/mtg/bin/vg", at 0x57ed93, in abort
     15 #0    Object "/home/mtg/bin/vg", at 0x12e27bb, in raise

vgteam / vg