search

maickrau / MBG

MIT License
57 stars 2 forks source link

Fails when reaching "Determinizing edges" #6

Closed nadegeguiglielmoni closed 2 years ago

nadegeguiglielmoni commented 3 years ago

Hello,

Thank you for this tool.

I have tried running MBG on several datasets, and several machines, but I keep running into the same error:

MBG bioconda 1.0.6
Parameters: k=201,w=171,a=1,u=2,t=1,errormasking=hpc,endkmers=no,blunt=no
Collecting selected k-mers
Reading sequences from hifi.fasta
152048428 total selected k-mers in reads
14578668 distinct selected k-mers in reads
Unitigifying
Filtering by unitig coverage
4588344 distinct selected k-mers in unitigs after filtering
Getting unitig sequences
Reading sequences from hifi.fasta
Determinizing edges
MBG: src/MostlySparse2DHashmap.h:50: BigType MostlySparse2DHashmap<SmallType, BigType>::get(std::pair<long unsigned int, bool>, std::pair<long unsigned int, bool>) const [with SmallType = short unsigned i
nt; BigType = long unsigned int]: Assertion `found != additionalKeyValues.end()' failed.
/var/slurmd-inter/job177121/slurm_script: line 29: 137490 Abandon                 (core dumped) /dss/dssfs02/lwp-dss-0001/pn69xe/pn69xe-dss-0000/user/ignite_tools_py3/.conda/envs/mbg/bin/MBG -i hifi.fasta -o MBG_default_k201 -k 201
gconcepcion commented 2 years ago

I ran into the same problem trying to do a coverage titration on a human dataset. The 10x datapoint worked, but got the same core dump as above with the higher coverage points.

Any idea what's going on here?

maickrau commented 2 years ago

Determinizing edges is no longer done in the latest version. Feel free to open a new issue if there is another crash