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VG autoindex does not work for gfa walks when the SeqStart or SeqEnd fields are equal to "*" #4517

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mir-cat opened this issue Feb 3, 2025 · 2 comments · May be fixed by #4523
Open

VG autoindex does not work for gfa walks when the SeqStart or SeqEnd fields are equal to "*" #4517

mir-cat opened this issue Feb 3, 2025 · 2 comments · May be fixed by #4523

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@mir-cat
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mir-cat commented Feb 3, 2025 •
edited
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1. What were you trying to do?
run vg autoindex on a pggb graph, after converting paths to walks.

2. What did you want to happen?
The indexes to be generated

3. What actually happened?
An error was thrown:

Parsing metadata
terminate called after throwing an instance of 'std::runtime_error'
  what():  MetadataBuilder: Invalid start position *

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 v1.63.1 "Boccaleone"
Caught signal 6 raised at address 0x22bce6c; tracing with backward-cpp
Stack trace (most recent call last):
#19   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x65e4f4, in _start
#18   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x2279136, in __libc_start_main
#17   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x2277899, in __libc_start_call_main
#16   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0xf2d5fb, in vg::subcommand::Subcommand::operator()(int, char**) const
#15   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0xd7e61e, in main_autoindex(int, char**)
#14   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x123ce55, in vg::IndexRegistry::make_indexes(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)
#13   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x122d76c, in vg::IndexRegistry::execute_recipe(std::pair<std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, unsigned long> const&, vg::IndexingPlan const*, vg::AliasGraph&)
#12   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x124522d, in std::_Function_handler<std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > (std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&), vg::VGIndexes::get_vg_index_registry()::{lambda(std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)#61}>::_M_invoke(std::_Any_data const&, std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*&&, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)
#11   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x1244e95, in vg::VGIndexes::get_vg_index_registry()::{lambda(std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)#61}::operator()(std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const [clone .constprop.0]
#10   Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x18527c6, in gbwtgraph::gfa_to_gbwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, gbwtgraph::GFAParsingParameters const&)
#9    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x1845507, in gbwtgraph::parse_metadata(gbwtgraph::GFAFile const&, std::vector<gbwtgraph::ConstructionJob, std::allocator<gbwtgraph::ConstructionJob> > const&, gbwtgraph::MetadataBuilder&, gbwtgraph::GFAParsingParameters const&)
#8    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x1843659, in gbwtgraph::GFAFile::for_these_walk_names(std::vector<char const*, std::allocator<char const*> > const&, std::function<void (std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)> const&) const
#7    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x5d49be, in gbwtgraph::MetadataBuilder::add_walk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long) [clone .cold]
#6    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x21b16b8, in __cxa_throw
#5    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x21b1556, in std::terminate()
#4    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x21b14eb, in __cxxabiv1::__terminate(void (*)())
#3    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x61b3eb, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#2    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x61db33, in abort
#1    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x2290315, in raise
#0    Object "/gpfs/project/projects/medbioinf/projects/mihen108/rdna_morphs/snakemake/wds/wd_morphs/.snakemake/conda/981958c9ce1696c12cffa5f58d856241_/bin/vg", at 0x22bce6c, in __pthread_kill

Library locations:
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
━━━━━━━━━━━━━━━━━━━━
Context dump:
	Thread 0: Starting 'autoindex' subcommand
Found 1 threads with context.
━━━━━━━━━━━━━━━━━━━━
Please include this entire error log in your bug report!

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

vg autoindex --workflow giraffe -g {gfa_with_walks} -p {prefix}

6. What does running vg version say?

vg version v1.63.1 "Boccaleone"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Using HTSlib headers 101990, library 1.19.1-29-g3cfe8769
Built by anovak@mustard

Given that "*" is a valid value in the specification for SeqStart or SeqEnd , I was surprised when an error was thrown. Is there a way that these values can be somehow derived, so as not to have to use "*"?
@jltsiren jltsiren reopened this Feb 4, 2025
@jltsiren
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jltsiren commented Feb 4, 2025 •
edited
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This will be fixed in the next vg release. Meanwhile, if you can compile vg yourself, you should be able to fix this by updating deps/gbwtgraph to the latest master.

If you can't compile vg, you can avoid the issue by setting SeqStart to 0.

jltsiren added a commit to jltsiren/vg that referenced this issue Feb 4, 2025
@jltsiren
Update GBWTGraph (see vgteam#4517)
9ff0ea8
@mir-cat
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mir-cat commented Feb 4, 2025

Thank you for your quick work on this!

@jltsiren jltsiren linked a pull request Feb 12, 2025 that will close this issue
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Sample fragmented haplotypes vgteam/vg
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@mir-cat @jltsiren