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SBR error (Read 1477 times)
Matt
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SBR error
Oct 31st, 2011 at 7:13am
 
I am trying to run a SBR analysis, and am getting an error message: I am running like this (my input and export files are defined elsewhere:
[code]/* SBR */

HYPHY_BASE_DIRECTORY = "/home/matthew/hyphy/HYPHY/";

stdinRedirect = {};
stdinRedirect ["00"] = "Codon";
stdinRedirect ["01"] = filepath;
stdinRedirect ["02"] = "Universal";
stdinRedirect ["03"] = "Run 2";
stdinRedirect ["04"] = "10000";
stdinRedirect ["05"] = "GY94";
stdinRedirect ["06"] = "Local";
stdinRedirect ["07"] = sbr;

batchFileToRun = HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "SingleBreakpointRecomb.bf";
ExecuteAFile  (batchFileToRun, stdinRedirect);[/code]

The error message I get is this: Any ideas about what to do?

[code]There are 66 potential breakpoints.
How many KH samples should be drawn per breakpoint ?
1). Single partition analysis
Log Likelihood = -2958.61339102045;
Shared Parameters:
kappa=0.334229

Tree givenTree=[tree info deleted for readability]

AIC  = 6595.23

c-AIC = 5701.74

BIC  = 8904.98
2). Looking for a breakpoint...

Breakpoint at position      2. dAIC =     -649.63 dAICc =      -2.83 dBIC =   -2952.57Error:
Cannot reuse the filter 'filteredData0' because it is already being used by likelihood function 'lf', and the two likelihood functions impose different leaf-to-sequence mapping. Create a copy the filter and pass it to the second likelihood function to resolve this issue.

Function call stack
1 : Construct the following likelihood function:filteredData0 ; j_tree_0 ; filteredData1 ; j_tree_1 ;
     Standard input redirect:
           Empty Associative List-------
2 : RunASample(individual)
     Standard input redirect:
           Empty Associative List-------
3 : ExecuteAFile from file batchFileToRun using basepath /home/matthew/Desktop/genus/hyphy/hyphy/. reading input from stdinRedirect
{"00":"Codon",
"01":"/home/matthew/Desktop/genus/seq/Forpub.fasta",
"02":"Universal",
"03":"Run 2",
"04":"10000",
"05":"GY94",
"06":"Local",
"07":"/home/matthew/Desktop/genus/hyphy/sbr.out"}
-------
matthew@macmanes:~/Desktop/genus/hyphy$
[/code]
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Sergei
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Datamonkeys are forever...

Posts: 1658
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Re: SBR error
Reply #1 - Oct 31st, 2011 at 10:52am
 
Hi Matt,

The analysis is currently broken (at least the KH option is); thanks for pointing this out. I would suggest you use GARDProcessor.bf ( in the interim. We are in the middle of a massive codebase overhaul, so many of these issues will go away. Sorry for the inconvenience.

Sergei
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