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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Assertion failure in CountPairedInfo() #573

Open epruesse opened 3 years ago

epruesse commented 3 years ago

I reproducibly get the below error with 3.14.0 and 3.14.1:

  0:00:41.211    85M / 6G    INFO    General                 (path_extender.hpp         : 894)  
 Processed 150 paths from 493 (30%)
spades-core: /opt/conda/conda-bld/spades_1596699678396/work/src/common/modules/path_extend/paired_library.hpp:131: 
double path_extend::PairedInfoLibraryWithIndex<Index>::
CountPairedInfo(path_extend::EdgeId, path_extend::EdgeId, int, bool) const
[with Index = const omnigraph::de::PairedIndex<debruijn_graph::DeBruijnGraph, omnigraph::de::PointTraits, 
omnigraph::de::safe_btree_map>&; path_extend::EdgeId = omnigraph::impl::EdgeId]: 
Assertion `index_.size() != 0' failed.

The data is admittedly pathological. It is a sample screened for a target genome using high-sensitivity mapping. The sample probably does not contain the genome, but due to high sensitivity mapping, there are still ~50k reads passed into spades.

I can't post the data here, but I am willing to help debug.

It's probably an edge case not relevant for "sane" situations, but it does break our pipeline when spades "crashes" on some negative samples.

asl commented 3 years ago

Will you please post your spades.log file?

epruesse commented 3 years ago

Here:

spades.log

ajkarloss commented 2 years ago

How did you solve this issue?