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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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exit_status 120 #1505

Closed minglibio closed 3 weeks ago

minglibio commented 1 month ago

Hi, I am running cactus v2.8.4 on a grid_engine cluster. It failed several times, but after restart, I have successfully run it until chain_one_alignment. In the previous failed runs, the main problem was to set up the memory, after I changed the memory set it usually solved the problem. But in the last two runs, it exited with the same exit_status 120 without any other info. So now I don't know how to proceed further. I am wondering if you have any ideas on this.

The command I used for the last run:

export TOIL_GRIDENGINE_PE='smp'
export TOIL_GRIDENGINE_ARGS='-q scc,long -l avx2,h_vmem=20G -S /data/scc3/ming.li/software/cactus-bin-v2.8.4/venv-cactus-v2.8.4/bin/python'
source /data/scc3/ming.li/software/cactus-bin-v2.8.4/venv-cactus-v2.8.4/bin/activate
cp /data/scc3/ming.li/software/cactus-bin-v2.8.4/venv-cactus-v2.8.4/bin/_toil_worker ./
cactus ./js ./cactus.list CactusAlign.hal --workDir ./temp --defaultMemory 150G --defaultCores 20 --consCores 20 --maxCores 24 --maxMemory 400G --doubleMem true --lastzCores 2 --lastzMemory 20G --realTimeLogging True --batchSystem grid_engine --manualMemArgs --restart

Attached are the logs of the last three runs.

logs.zip

minglibio commented 3 weeks ago

Added more memory and rerun solved this issue.