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HYPHY Package >> HyPhy bugs >> Bug in FUBAR stage 4

Message started by EricE on Apr 9th, 2013 at 8:53am

Title: Bug in FUBAR stage 4
Post by EricE on 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":_fubarMCMCSamplesLocation,"3":""+_fubarChainCount,"4":_fubarResultLocation,"5":_fubarSimFitFile,"6":_fubarSimGrid,"7":_fubarCodonFitLocation}

Title: Re: Bug in FUBAR stage 4
Post by Sergei on 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 :


$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.


Title: Re: Bug in FUBAR stage 4
Post by EricE on Apr 10th, 2013 at 6:29am
Thanks it works now.


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