Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
SBR error (Read 2089 times)
YaBB Newbies

Feed your monkey!

Posts: 23
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:

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
"03":"Run 2",
Back to top
IP Logged
YaBB Administrator

Datamonkeys are forever...

Posts: 1658
Gender: male
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.

Back to top

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
IP Logged