qpAdm sometimes copies admixture proportions in other lines,about dreichlab/admixtools

TCLamnidis commented on July 21, 2024

I should add, as far as I can see, this happens consistently with certain sample sets, copying over the same models every time (at least in my 3 replicates).

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bumblenick commented on July 21, 2024

This does look like a bug. Does it ever happen when the model is "feasible" A workaround of course is to rerun deleting sources you don't want, and rerun. Please tell me the version number (grep on version: in logfile) N

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On Thu, Apr 27, 2017 at 11:17 AM, TCLamnidis ***@***.***> wrote: Hello! Sometimes qpAdm will give me identical admixture proportions between different models, and even forego forcing some to 0. (see part of results below). I am fairly sure the chi square statistics are accurate for the model, I just don't get the admixture proportions. fixed pat wt dof chisq tail prob 00000 0 4 2.925 0.570392 0.006 -0.022 0.557 0.048 0.411 infeasible 00001 1 5 101.589 2.44391e-20 -4.084 0.558 0.092 4.434 0.000 infeasible 00010 1 5 3.026 0.696022 -4.084 0.558 0.092 4.434 0.000 infeasible 00100 1 5 83.532 1.52896e-16 -4.084 0.558 0.092 4.434 0.000 infeasible Clearly in the latter 2 models, the final component shouldn't be forced to 0, and instead the other components should. Is this a problem with my use, or an internal problem? Cheers — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#24>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h-uM1qn8bZmmsEOE5kFXHtHfXTPqks5r0LF3gaJpZM4NKXcQ> .

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TCLamnidis commented on July 21, 2024

## qpAdm version: 610

Yes, it also happens with feasible models:

        00000  0     2     4.803       0.0905804     0.592     0.097     0.183     0.101     0.028 
        00001  1     3    17.570     0.000539394     0.493     0.098     0.210     0.199     0.000 
        00010  1     3     7.677       0.0531877     0.493     0.098     0.210     0.199     0.000

And it seems to overwrite models that are not rejected too, since in the first example one of the models had a high tail probability.

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bumblenick commented on July 21, 2024

I think I found the problem and am in the process of fixing. It likely is caused by having 2 populations in the left set that are very very similar genetically. Is that plausible here? Nick

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On Thu, Apr 27, 2017 at 12:36 PM, TCLamnidis ***@***.***> wrote: ## qpAdm version: 610 Yes, it also happens with feasible models: 00000 0 2 4.803 0.0905804 0.592 0.097 0.183 0.101 0.028 00001 1 3 17.570 0.000539394 0.493 0.098 0.210 0.199 0.000 00010 1 3 7.677 0.0531877 0.493 0.098 0.210 0.199 0.000 And it seems to overwrite models that are not rejected too, since in the first example one of the models had a high tail probability. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h9etoUH6tIlzT-Q5BmJObYHPAHJbks5r0MQYgaJpZM4NKXcQ> .

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TCLamnidis commented on July 21, 2024

Here, the five source left populations are genetically distinct. Moreover, they remain mostly intact across multiple analyses, the changing variable being the population being explained as a 5-way mixture. Only specific target populations seem to trigger this effect, while most run normally without copied lines in the outputs.

Note: I have managed to run the reduced models without problem, as you suggested.

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bumblenick commented on July 21, 2024

I just pushed a new version of Admixtools to github. Probably this fixes your problem. Please let me know! Nick

…

On Thu, Apr 27, 2017 at 11:17 AM, TCLamnidis ***@***.***> wrote: Hello! Sometimes qpAdm will give me identical admixture proportions between different models, and even forego forcing some to 0. (see part of results below). I am fairly sure the chi square statistics are accurate for the model, I just don't get the admixture proportions. fixed pat wt dof chisq tail prob 00000 0 4 2.925 0.570392 0.006 -0.022 0.557 0.048 0.411 infeasible 00001 1 5 101.589 2.44391e-20 -4.084 0.558 0.092 4.434 0.000 infeasible 00010 1 5 3.026 0.696022 -4.084 0.558 0.092 4.434 0.000 infeasible 00100 1 5 83.532 1.52896e-16 -4.084 0.558 0.092 4.434 0.000 infeasible Clearly in the latter 2 models, the final component shouldn't be forced to 0, and instead the other components should. Is this a problem with my use, or an internal problem? Cheers — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#24>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h-uM1qn8bZmmsEOE5kFXHtHfXTPqks5r0LF3gaJpZM4NKXcQ> .

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TCLamnidis commented on July 21, 2024

I tried rerunning some of the models that had problems before, and all mixture proportions are printed normally now.

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bumblenick commented on July 21, 2024

Great; I think you have a boundary case in which some populations have very thin data. In the new release I trap these cases and do something (fairly) reasonable. Nick

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On Tue, May 16, 2017 at 5:20 AM, TCLamnidis ***@***.***> wrote: I tried rerunning some of the models that had problems before, and all mixture proportions are printed normally now. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_hxlnrt9DeEXAGRh43h8E8QU-XJCWks5r6WpAgaJpZM4NKXcQ> .

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