core dump when runing pathracer

[yjk-bertrand]

Description of bug

Running pathracer on an assembly graph generated from SPAdes4 and a DNA hmm profile, makes it crash after extracting the unique edge paths.
test_data.zip
An empty .edges.fa file gets generated along a .seqs.fa file that contains matching paths in the graph.
Crash reports is the following:
=== Stack Trace ===
pathracer() [0x44e1a9]
pathracer() [0x456f9d]
pathracer() [0x46f477]
pathracer() [0x46f7a1]
pathracer() [0x42ad6e]
pathracer() [0x4469aa]
/lib/x86_64-linux-gnu/libgomp.so.1(+0x1dc0e) [0x7bfeb010cc0e]
/lib/x86_64-linux-gnu/libc.so.6(+0x94ac3) [0x7bfeafa94ac3]
/lib/x86_64-linux-gnu/libc.so.6(+0x126850) [0x7bfeafb26850]
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const'. In file '/__w/spades/spades/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 3 -> 11 was not found for vertex 22'.
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const'. In file '/__w/spades/spades/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 3 -> 11 was not found for vertex 22'.
pathracer: /__w/spades/spades/src/common/assembly_graph/core/graph.h
pp:141: size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const: Assertion `false' failed.

spades.log

pathracer.log.zip

params.txt

params.txt

SPAdes version

SPAdes-4.0.0-Linux

Operating System

Linux

Python Version

Python 3.12.2

Method of SPAdes installation

manual

No errors reported in spades.log

• Yes

[asl]

Will you please upload the graph and the query to reproduce issue?

Thanks!

[asl]

Ah, sorry, see it attached as test_data