ablab
core dump when runing pathracer
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
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
- [X] Yes
