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maickrau / MBG

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UnitigResolver.cpp:3971 resolveRound Assertion 'topSize < maxLocalResolve' failed #29

Open grinning-bat opened 5 months ago

grinning-bat commented 5 months ago

Hello again! I have another issue. It's repeatable - I have 3 different datasets failing with the same error.

Here is the error message from the same dataset as in #28 

MBG: src/UnitigResolver.cpp:3971: void MBG::resolveRound(ResolvableUnitigGraph&, std::vector&, size_t, size_t, size_t, bool, bool, size_t, bool, std::ostream&): Assertion `topSize < maxLocalResolve' failed.
./buildGraph.sh: line 41: 1582179 Aborted                 (core dumped) [redacted]/verkko/env/lib/verkko/bin/MBG $iopt -t 10 -k 1003 -r 15000 -R 4000 -w 100 --kmer-abundance 1 --unitig-abundance 2
--error-masking=collapse-msat --output-sequence-paths ../1-buildGraph/paths.gaf --hpc-variant-onecopy-coverage 25 --do-unsafe-guesswork-resolutions --out ../1-buildGraph/hifi-resolved.gfa

The rest of buildGraph.err :

MBG Branch master commit c26721b2de0b6f3785deb8922a0e14cab04c2291 2024-02-17 14:57:10 +0200
Parameters: k=1003,w=100,a=1,u=2,t=10,r=15000,R=4000,hpcvariantcov=25,errormasking=collapse-msat,endkmers=no,blunt=no,keepgaps=no,guesswork=yes,copycountfilter=no,onlylocal=no,filterwithinunitig=yes,cleaning=yes,cache=no
Collecting hpc variant k-mers
Reading sequences from ../hifi-corrected.fasta.gz
462177078 total selected k-mers in reads
121404204 distinct selected k-mers in reads
Reading sequences from ../hifi-corrected.fasta.gz
Collecting selected k-mers
Reading sequences from ../hifi-corrected.fasta.gz
462177078 total selected k-mers in reads
121412362 distinct selected k-mers in reads
Unitigifying
Filtering by unitig coverage
8314157 distinct selected k-mers in unitigs after filtering
Getting read paths
Reading sequences from ../hifi-corrected.fasta.gz
Resolving unitigs
1018326 unitigs before resolving
estimated average coverage 6.53827
3898659 raw read paths
3937992 raw read paths
1710623 read paths
removed 16706 tips
removed 68 crosslinks
removed 405 nodes and 0 edges

I managed to get core dump this time, unfortunately it's truncated to 2G (uploaded to ftp)

6503e6823bfad1f81a60939e20e07247  core.MBG.1582179.lz4
maickrau commented 5 months ago

The log seems to show it's commit c26721b which is not the latest. Could you try recompiling the latest commit of MBG (currently 10782bd) and rerunning with that? You might also need to do make clean and git submodule update --init --recursive before make all