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odgi build Assertion '!has_node(id)' failed #590

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cwatt opened this issue Sep 4, 2024 · 0 comments
Open

odgi build Assertion '!has_node(id)' failed #590

cwatt opened this issue Sep 4, 2024 · 0 comments

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@cwatt
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cwatt commented Sep 4, 2024

Hello, I'm experiencing this error and am creating a new issue for visibility. I installed odgi via bioconda. Unfortunately, odgi version doesn't print anything, but I assume the version is 0.8.6-2 according to the current bioconda recipe.

What I did:
I constructed a graph of a single chromosome using minigraph-cactus and converted the resulting v1.1 .gfa file to v1.0 via
vg convert -gfW graph.gfa -t 30 > graph_v1.0.gfa

I then attempted to build the .og file...
odgi build -g graph_v1.0.gfa -o graph.og -s -t 30

... But received this error
odgi: /opt/conda/conda-bld/odgi_1623932587958/work/src/odgi.cpp:507: virtual handlegraph::handle_t odgi::graph_t::create_handle(const string&, const nid_t&): Assertion '!has_node(id)' failed.

The nodes are unique

grep "^S" graph_v1.0.gfa | cut -f 2 | wc -l
5745440
grep "^S" graph_v1.0.gfa | cut -f 2 | uniq | wc -l
5745440

And the .gfa file is valid

vg validate graph_v1.0.gfa
graph: valid

I also tried constructing the .og using the v1.1 .gfa file with the same result, in case the conversion was the issue. Lastly, I tried running og build with only 1 thread because I saw that suggestion in the thread, but no luck.

I'm not sure what the problem is or how else to troubleshoot. Any help would be appreciated!

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