memory allocation warning trying run msat analysis

[Chaffee, Carol [EEOBS]]

I’m trying to run a fairly small msat dataset (3 pops, 209 individuals, 5 loci) on a 1600 MHz, 1.7 GHz MacBook Air with 8 GB RAM running Mavericks (10.9.1). I keep getting an error “WARNING in memory allocation (malloc(0)) in file tree.c on line <alternates between 900 & 2700>” until I kill the process. I’ve seen in the archives that similar errors are related to the infile using the wrong encoding. My original file was UTF-8, but I’ve used iconv to convert it to US-ASCII. I’ve attached my infile & parmfile. Any thoughts on how to resolve this error?

Thanks,

Carol

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Carol L. Chaffee, PhD

HHMI Post-Doctoral Teaching Fellow

208 Bessey Hall

Dept. of Ecology, Evolution & Organismal Biology

Iowa State University

Ames, IA 50011

[Peter Beerli]

Carol,

you have set the value called ‘micro-threshold’ to zero, this will lead to problems in the calculation of the likelihood during the run,

the default is 200 for the singlestep and the multistep model, it seems that a threshold of 10 works also for your data, but:

- I suggest to not use the singlestep mutation model, because it is __glacially slow__ for real runs and does not deliver ‘better’ estimates than the Brownian mutation model (see Beerli 2007). 

- You need to adjust the upper prior boundary for Theta and M, see also attached parmfile

Peter

[Chaffee, Carol [EEOBS]]

Thanks Peter, it runs now!

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