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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Locally running cactus is very time-consuming ! #89

Open bioinformaticspcj opened 5 years ago

bioinformaticspcj commented 5 years ago

Dear the authors: Thanks for developing such a useful program. I just try to run cactus locally on Centos 7 with the example data，the commend is "cactus jobStore2 --restart --root mr --binariesMode local examples/evolverMammals1.txt examples/evolverMammals.hal --maxCores 112 --maxDisk 500G" But it takes far more than an hour to finish the job. It actually takes 40 hours. I do not know why it is that slow and does not perform as you have just said.

Looking forward to your valuable replies.

VidJa commented 5 years ago

I'm experiencing the same thing. the evolverMammals example took 4 hours on with --maxCores 60 --maxDisk 1024G My two plant genomes (~950Gb) are running now for 4 days on the same system The gridengine runs stalled after one hour and never finished. Is this to be expected?