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problems with multithread version #69

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gargkritika opened this issue Jul 18, 2020 · 1 comment
Open

problems with multithread version #69

gargkritika opened this issue Jul 18, 2020 · 1 comment

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@gargkritika
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Dear Dr. Gronau,

I have been using G-PhoCS for my work and have issues with the multithread version only. I have a complex model of gene flow between multiple lineages based on D-statistics. Based on the D statistics estimates I have been performing test runs for my dataset. I was able to run G-PhoCS successfully.

However, when I was going through my trace file, I observed two columns with tau estimates for current populations (in this case they are called phi and sul). The values for these estimates are zero. I am not sure why these columns are present. When I run the same files with the single core version, I do not observe these columns.

It would be really helpful, if you can help me debug this. I have attached
subset_trace.log
a sample of my trace file for your reference.

Thank you very much.

Best Regards,
Kritika

@igronau
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igronau commented Jul 19, 2020

The tau parameters for sampled populations are actually used when you wish to model ancient samples, and then the tau parameter corresponds to the time in which these samples died. This can be set (by your prior knowledge) or estimated. However, these parameters should be defined only if you define an "age" attribute in the relevant CURRENT_POP, and I couldn't see that in your control file. And there really shouldn't be any difference between the multithreaded version and the single thread version. Are you using the latest public version from Github?The log files should indicate if G-PhoCS detected these populations as "ancient". We may be able to figure out what happened by looking at that.Anyway, as long as the values remain 0, then this shouldn't influence the sampler in any way. It's as if you defined these populations as ancient, but then fixed their time as current time.

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