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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Assertion `reference_for.count(fasta_contig)' failed. #3702

Open 8banzhuan opened 2 years ago

8banzhuan commented 2 years ago

Hi I'm having a little trouble trying to build a vg graph I tried to build with the following command I provided GRC38 and its VCF file ./vg construct -r fa/GRCh38_latest_genomic.fna -v vcf/GRCh38_latest_clinvar.vcf > gfa/human.vg He gives the following error vg: src/constructor.cpp:2230: void vg::Constructor::construct_graph(const std::vector<FastaReference>&, const std::vector<vcflib::VariantCallFile>&, const std::vector<FastaReference*>&, const std::function<void(vg::Graph&)>&): Assertion reference_for.count(fasta_contig)' failed. 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_JCvAIz/stacktrace.txt Please include the stack trace file in your bug report! The content in stacktrace.txt is Crash report for vg v1.38.0 "Canossa" Stack trace (most recent call last):

10 Object "/home/yaozhen/vg", at 0x5b635d, in _start

9 Object "/home/yaozhen/vg", at 0x1cb357f, in __libc_start_main

8 Object "/home/yaozhen/vg", at 0x58a62e, in main

7 Object "/home/yaozhen/vg", at 0xbf999b, in vg::subcommand::Subcommand::operator()(int, char**) const

6 Object "/home/yaozhen/vg", at 0xbb6076, in main_construct(int, char**)

5 Object "/home/yaozhen/vg", at 0xd1d161, in vg::Constructor::construct_graph(std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::function<void (vg::Graph&)> const&)

4 Object "/home/yaozhen/vg", at 0xd1c541, in vg::Constructor::construct_graph(std::vector<FastaReference, std::allocator<FastaReference> > const&, std::vector<vcflib::VariantCallFile, std::allocator<vcflib::VariantCallFile> > const&, std::vector<FastaReference, std::allocator<FastaReference> > const&, std::function<void (vg::Graph&)> const&)

3 Object "/home/yaozhen/vg", at 0x1cc3855, in __assert_fail

2 Object "/home/yaozhen/vg", at 0x589a23, in __assert_fail_base.cold

1 Object "/home/yaozhen/vg", at 0x589b53, in abort

0 Object "/home/yaozhen/vg", at 0x136b1cb, in raise

` Excuse me, thank you

jeizenga commented 2 years ago

Can you verify that all of the chromosomes have the same name in both the FASTA and the VCF? For instance, you might have the sequence called chr12 in the FASTA and 12 in the VCF.