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Parameter List Out of Context Error (Read 2163 times)
EmmaH
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Parameter List Out of Context Error
Oct 16th, 2012 at 5:52am
 
Dear all,
I am trying to run GADatedClock.bf, but am encountering an error I don't really understand.

I'm using a GRM or HKY85 (I've tried both) model, with 'Local' model parameters. However, when I try to constrain 'All Parameters', I get the errors:

Quote:
Master node received an error:Parameter list is out of context:clockTree.66_H3N2_Hong_Kong_Hong_Kong_1_4_MA21_1_1968.f,?e,d,c,b,a:=cloc
kTree_scaler_0*(1.968-clockTree_Node0_T)
(for GRM)

Quote:
Master node received an error:Parameter list is out of context:clockTree.66_H3N2_Hong_Kong_Hong_Kong_1_4_MA21_1_1968.b,?a:=clockTree_sc
aler_0*(1.968-clockTree_Node0_T)
(for HKY85)

If I instead choose to constrain parameter 'a', the run completes successfully. However, I don't really understand what the lettered parameters stand for (what am I constraining when I constrain 'a'?).

Any help would be appreciated.

Thanks,
Emma

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Sergei
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Re: Parameter List Out of Context Error
Reply #1 - Oct 16th, 2012 at 3:47pm
 
Hi Emma,

Please use the "Global" model option. GADatedClock.bf is not a polished analysis file (sorry!), so not all options work as expected.

Sergei
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EmmaH
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Re: Parameter List Out of Context Error
Reply #2 - Oct 18th, 2012 at 9:22am
 
Dear Sergei,
Thank you, this seems to work fine - and is giving more sensible answers!

However, is there any difference to how I enter the date? Right now I am simply using year (1980, 2001, etc). Would it be better to use days (since some arbitrary date) or years since an arbitrary date?

I'm asking because I am confused about some of the output I am getting from GADatedClockProcess.bf - is there anywhere where there is more information about the files output?

In the .ps files, my dates vary but the root is far too old for my flu sequences (1600s or even 1200s). However, in the .nwk tree file (first tree), the node age/node height displayed in FigTree for the root is 39 - and 40 years ago would be about right for these sequences. Are the .ps files or the .nwk file right, and why the discrepancy?

Thanks for your help, and sorry for so many questions.
Emma
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