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ekg / seqwish

alignment to variation graph inducer
MIT License
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Aborted (core dumped) when building graph from 8 yeast genomes #30

Closed subwaystation closed 4 years ago

subwaystation commented 4 years ago

Hi @ekg ,

I tried to induce a variation graph from one fasta file with 8 yeast genomes via

ubuntu@pantograph2:~/sh$ ../software/seqwish/git/seqwish-0.1/bin/seqwish -s yeast_l10k_R64-1-1.fa -t 28 -g yeast_l10k_R64-1-1.gfa
seqwish: /home/ubuntu/vol1/software/seqwish/git/seqwish-0.1/src/main.cpp:98: int main(int, char**): Assertion `false' failed.
Aborted (core dumped)

As you suggested I went vg view -- vg paths -- cat new.fasta vg_paths.fasta. The .fa.fai of the new .fasta looks quite good. But seqwish just stops. I expect that it could be a naming scheme problem within the fasta headers?

You can get all the relevant data via wget http://fex.belwue.de/fop/Q60OHDwU/seqwish_yeast_ggbhtu2k19.tar.gz

Thanks for your feedback!

ekg commented 4 years ago

The problem is that you're not supplying any PAF file defining the alignment. I thought this was checked, but it looks like I wasn't careful.

You'll need to make that via something like scripts/pan-minimap2 or minimap2 -X -c -x asm20.

subwaystation commented 4 years ago

So I can't read your README. Will try that tomorrow.

subwaystation commented 4 years ago

So the error was on my side.