error: "Matrix names doesn't match"

[GoogleCodeExporter]

Thanks very much for your help!

What steps will reproduce the problem?
running the command: java -jar prottest-3.2.jar -i example.phy -all

What is the expected output? 

A selection of the best model

What do you see instead?
It runs through most of the models, then chokes on:

PHYML: . Model of amino acids substitution:     Custom 
(/global/home/users/icclark/pgms/prottest3/models/FLU)
Last token: (/global/home/users/icclark/pgms/prottest3/models/FLU)
It should be: FLU
Matrix names doesn't match
Model optimization exception: there was an error while executing cannot find 
FLU matrix description
Model................................ : FLU
  Number of parameters............... : 53 (0 + 53 branch length estimates)

What version of the product are you using? 
prottest-3.2

On what operating system?
CentOS5.8 (Linux 2.6.18).

Please provide any additional information below.

I compiled phyml from source and linked it to bin/phyml-prottest-linux because 
of a glibc2.7 error. After that, things run fine until prottest3 chokes on the 
FLU matrix. 

Original issue reported on code.google.com by iain.c.c...@gmail.com on 1 Sep 2012 at 5:22

[GoogleCodeExporter]

Could you please check if you have a "models" folder containing the FLU matrix 
in your ProtTest home directory?

Sorry for the late response, but the issue tracking in the repository was not 
propertly configured and I didn't realize about this report.

Original comment by DiegoDL84 on 17 Dec 2012 at 3:23

• Changed state: Accepted

[GoogleCodeExporter]

Hey,

Thanks for your email and sorry for the late response, I was hiking in Nepal.

I do have a models folder with FLU in it. Not sure why prottest can't
find it. To get around the issue I ended up feeding in all the models
besides FLU on the command line.

Happy New Year!
Iain

Original comment by iain.c.c...@gmail.com on 2 Jan 2013 at 4:09