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.
I reproducibly get the below error with 3.14.0 and 3.14.1:
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.