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Old 03-20-2014, 04:32 AM   #1
JdeBruin
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Location: South Africa

Join Date: Jun 2013
Posts: 25
Default CEGMA : Genewise Error

Hi all,

I am trying to run CEGMA and I am getting the following error message that has me lost:
Warning Error
Unable to open gene.stat as gene stats file
Warning Error
Could not read gene statistics in gene.stat
Warning Error
Could not open BLOSUM62.bla as a filename for read Blast matrix
Warning Error
Could not open file codon.table as codon table file
Warning Error
Could not read codon table file in codon.table
Fatal Error
Could not build objects!

Any help would be appreciated.
Thanks
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Old 03-21-2014, 08:10 AM   #2
kbradnam
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Location: Davis, CA

Join Date: May 2011
Posts: 53
Default

Can you please post the full output of CEGMA, including the command that you ran?

Also...do you have the latest versions of CEGMA, GeneWise, BLAST+ etc.

Regards,

Keith
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Old 05-01-2014, 03:10 AM   #3
philipp.bayer
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Location: Australia

Join Date: May 2014
Posts: 2
Default

Hi,

I know this is a bit late but I just stumbled over this error today so I thought I'd make an account and post the solution.

In my case, the environment variable WISECONFIGDIR was set incorrectly.

I "fixed" that by downloading my own installation of wise, since genewise was already installed system-wide, from here : http://korflab.ucdavis.edu/Datasets/...2.3-rc7.tar.gz

Then extracted it in my home directory, and set WISECONFIGDIR to the wisecfg/ subfolder of the extracted folder:

export WISECONFIGDIR=/home/bla/wise2.2.3-rc7/wisecfg

Now CEGMA works. This uses of course the system-wide installation of genewise.

(As a sidenote: You can save some time by running CEGMA with the -ext flag, that way CEGMA will continue roughly from where it crashed - but might continue on incomplete results!)

Last edited by philipp.bayer; 05-01-2014 at 03:13 AM.
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