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);

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$

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