I cant get .vg file using vg construct

NahlaHu commented 4 months ago

1. What were you trying to do?

2. What did you want to happen? get file.vg

3. What actually happened? 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_rJP2cN/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:

Place stacktrace here.

5. What data and command can the vg dev team use to make the problem happen? vg construct -r file.fa -v file.vcf.compressed.gz > file.vg

6. What does running vg version say?

Place vg version output here

jeizenga commented 4 months ago

I believe this is a case where the sequence names in your FASTA don't match the sequence names in your VCF. It should probably give a more informative warning though.

NahlaHu commented 4 months ago

Thank you.. I fixed it.

I have another question, what do you use for pangenome visualization?

vgteam / vg

I cant get .vg file using vg construct #4225