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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
420 stars 38 forks source link

different ranks? #20

Open cistarsa opened 4 years ago

cistarsa commented 4 years ago

Hello. I'm a user of minimap so I was relieved to see this new program! Anyway, I'm looking to generate a reference graph from 4 whole genome assemblies that were constructed using different assemblers from different individuals (obvi). But I'm coming into some issues. Do the contig/scaffold names affect the graph generation and what does this error from ./gfatools stat means can I resolve it? 

[W] stable sequence 'tig00006712' associated with different ranks on segment 's621820': 1 != 2

Ultimately, I'll have to convert this gfa to a vg file in order to map and call variants (as this isn't yet available, here?)

Thanks!

lh3 commented 4 years ago

The input sequences should all have different names.