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marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
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beta2: MBG assert #58

Closed skoren closed 2 years ago

skoren commented 2 years ago

Running a cattle genome, I get the following errors:

MBG: src/UnitigResolver.cpp:2249: void maybeTrim(ResolvableUnitigGraph&, std::vector<PathGroup>&, size_t, std::pair<long unsigned int, bool>, size_t): Assertion `maxReadTrim <= maxTrim' failed.
/var/spool/slurm/slurmd/job34357082/slurm_script: line 32: 33178 Aborted                 /data/korens/devel/verkko/lib/verkko/bin/MBG $iopt -t 4 -k 1001 -r 15000 -R 4000 -w 100 --kmer-abundance 1 --unitig-abundance 2 --error-masking=collapse-msat --output-sequence-paths ../1-buildGraph/paths.gaf --out ../1-buildGraph/hifi-resolved.gfa

This is using v1.0.9. The corrected reads are on biowulf in /data/korens/test/mikko_cns/cattle/

oushujun commented 2 years ago

Seems like many assertion errors for the new MBG version: https://github.com/maickrau/MBG/issues/13

skoren commented 2 years ago

The latest MBG crashes with:

MBG: src/UnitigResolver.cpp:479: std::pair<UnitigGraph, std::vector<ReadPath> > resolvableToUnitigs(const ResolvableUnitigGraph&, const std::vector<PathGroup>&): Assertion `result.unitigCoverage[i][j] > 0' failed.

which is identical to #57 so I think these are the same issue. Will close this one to avoid duplication.