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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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position X+Y is not inside node X #4250

Open Kled111 opened 3 months ago

Kled111 commented 3 months ago

I have successfully done with this command -- " vg giraffe -Z hprc-v1.1-mc-chm13.gbz -d /hprc-v1.1-mc-chm13.dist -m hprc-v1.1-mc-chm13.min -p -t 64 -f xxx.fastq > map.gam" but when I try to do variant calling with this command -- "vg augment chr22.vg map.gam -m 4 -q 5 -Q 5 -s -A chr22_aug.gam > chr22_aug.vg", it failed. This is the Crash report for vg v1.55.0 "Bernolda" forwardize_breakpoints error: failure, position 45209079-3 is not inside node 45209079 vg: src/augment.cpp:514: std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > > vg::forwardize_breakpoints(const HandleGraph*, const std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > >&): Assertion `false' failed. ━━━━━━━━━━━━━━━━━━━━ What should I do?

adamnovak commented 2 months ago

What is the relationship between hprc-v1.1-mc-chm13.gbz and chr22.vg? Are you sure that map.gam contains reads that reference nodes in chr22.vg and only nodes in chr22.vg?