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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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mAlloc in rule simplify #84

Closed KimSummers closed 4 years ago

KimSummers commented 4 years ago

Rule simplify with output: assembly/high_res/simplified.gfa log: assembly/high_res/simplification.log (check log file(s) for error message) shell: /mnt/gpfs/kim/Programs/STRONG/COG_pipe/../SPAdes/assembler/build/release/bin/spades-gsimplifier assembly/high_res/graph_pack assembly/high_res/simplified --gfa -k 77 --read- length 150 -t 16 --tmpdir assembly/high_res/tmp &> assembly/high_res/simplification.log

gives an mAlloc error Contents of implication.log are 0:00:00.000 24M / 24M INFO General (main.cpp : 134) Starting SPAdes-based standalone graph simplifier, built from N/A, git revision N/A 0:00:00.013 25M / 25M INFO General (main.cpp : 143) K-mer length set to 77 0:00:00.013 25M / 25M INFO General (main.cpp : 148) # of threads to use: 16 0:00:00.013 25M / 25M INFO General (main.cpp : 152) Loading de Bruijn graph from assembly/high_res/graph_pack

: Error in malloc(): out of memory Requested: 3933401693298884616
Sebastien-Raguideau commented 4 years ago

issue not replicable. Due to bad install/previous install/previous version/....