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Bug in FUBAR stage 4 (Read 2905 times)
EricE
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Bug in FUBAR stage 4
Apr 9th, 2013 at 8:53am
 
When running FUBAR with the test data on the HyPhy 2.1.2 release it fails on stage 4.

FUBAR was run with default parameters and HyPhy was install make MP2 and make install.

The following is the error message encountered.

Processing samples from chain 0/5 0Error:
Operation '/' is not implemented/defined for a Matrix

Function call stack
1 : pos_sel_matrices+(thisSample*(site_probs["conditionals"]$positive_selection_stencil)/norm_matrix)
     Standard input redirect:
           Empty Associative List-------
2 : tabulateGridResults(points,sites,samples,_chainCount)
     Standard input redirect:
           Empty Associative List-------
3 : ExecuteAFile from file Join(DIRECTORY_SEPARATOR,{{PATH_TO_CURRENT_BF[0][Abs(PATH_TO_CURRENT_BF)-2],"FUBAR_HBL","FUBAR_PHASE_4.bf"}}) using basepath /share/apps/FUBAR/. reading input from {"0":_fubarNucFitLocation,"1":_fubarGridInfoLocation,"2":_fubarMCMCSamplesLocati
on,"3":""+_fubarChainCount,"4":_fubarResultLocation,"5":_fubarSimFitFile,"6":_fu
barSimGrid,"7":_fubarCodonFitLocation}
-------

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Sergei
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Datamonkeys are forever...

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Re: Bug in FUBAR stage 4
Reply #1 - Apr 9th, 2013 at 3:53pm
 
Hi Eric,

You need a newer version of HyPhy -- 2.1.2 is about a year old and is no longer actively developed. Please use the hyphyqt branch :

Code:
$git clone git@github.com:veg/hyphy.git
$git checkout hyphyqt
$cmake ./
$make MP2
$make install

 



I'll update the wiki page to reflect this.

Sergei
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Division of Infectious Diseases
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EricE
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Re: Bug in FUBAR stage 4
Reply #2 - Apr 10th, 2013 at 6:29am
 
Thanks it works now.

-Eric
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