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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.
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!
The text was updated successfully, but these errors were encountered:
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
And the .gfa file is 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!
The text was updated successfully, but these errors were encountered: