Dear List:
Pardon me if this is an inappropriate place for this question, but I am having a problem executing program BOTTLENECK (Cornuet and Luikart 1997). For one very rich microsatellite locus, the program is unable to get past calculation of He. For the calculation of Heq, it tries various values of theta for likelihood, which for this locus hasn't exceeded about 0.040. This apparently prompts it to try again, giving the following error message: "Maybe a bad interval. Be patient, I try again [sic] ..." It has tried thousands of times over about four days and always fails. The same locus in another population worked fine. I am using the TPM model, the variance set at 12, proportion of SMM in TPM is 90, and 1000 iterations. There are about 450 individuals in this population, about 250 in the population where this locus had no problems. Any suggestions? Is there a hard-coded minimum likelihood value that I could relax? Should I try more iterations? Based on Figure 2 in Luikart and Cornuet and the richness of this allele (k=73) perhaps I need to have it exploring larger values of theta (it currently usually tries between 100 and 1000)?
Thank you for your time.
Steve
Pardon me if this is an inappropriate place for this question, but I am having a problem executing program BOTTLENECK (Cornuet and Luikart 1997). For one very rich microsatellite locus, the program is unable to get past calculation of He. For the calculation of Heq, it tries various values of theta for likelihood, which for this locus hasn't exceeded about 0.040. This apparently prompts it to try again, giving the following error message: "Maybe a bad interval. Be patient, I try again [sic] ..." It has tried thousands of times over about four days and always fails. The same locus in another population worked fine. I am using the TPM model, the variance set at 12, proportion of SMM in TPM is 90, and 1000 iterations. There are about 450 individuals in this population, about 250 in the population where this locus had no problems. Any suggestions? Is there a hard-coded minimum likelihood value that I could relax? Should I try more iterations? Based on Figure 2 in Luikart and Cornuet and the richness of this allele (k=73) perhaps I need to have it exploring larger values of theta (it currently usually tries between 100 and 1000)?
Thank you for your time.
Steve