memory consumption of MSMC

[hhu1]

I was running MSMC on 4 genomes (8 haplotypes) from the same human population. I was particularly interested the demographic history in the last 30,000 years. After converting the data into appropriate input file of MSMC, it is around 300 MB.

The issue is that MSMC is consuming too much memory now. On our 256GB server, it rapidly took all the memory and got terminated by the system daemon. If I instead run on chr22 only (4.1MB input file), it runs fine but took 4 GB RAM.

My question is that, is there a way I can reduce the memory usage and still get a decent resolution on demographic history in the last 30,000 years? If not, would you recommend reducing the number of chromosomes or the number of haplotypes included in the MSMC run? I.e., which option compromises the accuracy of the results least?

Thanks very much for your help,
Hao Hu

[stschiff]

Try to run it first on 4 haplotypes, using the -I flag to pick the haplotypes you want. With 8 haplotypes and two subpopulations it uses quite a bit of memory, but I have usually found 80Gb to be enough. How many cores are you running in parallel? I use 10 usually. With more cores you need more memory.

[hhu1]

I used the default -t. It looks that if I set -t to 10, MSMC is using 75 Gb and runs well so far. Thanks for the help!

Best,
Hao

On May 19, 2015, at 3:27 AM, Stephan Schiffels notifications@github.com wrote:

Try to run it first on 4 haplotypes, using the -I flag to pick the haplotypes you want. With 8 haplotypes and two subpopulations it uses quite a bit of memory, but I have usually found 80Gb to be enough. How many cores are you running in parallel? I use 10 usually. With more cores you need more memory.

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