Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
Ugene 1.20 Error with external tools (Read 4921 times)
Feb 11th, 2016 at 4:35am

AK   Offline
YaBB Newbies

Posts: 14
*
 
Hi,

I am using Ubuntu 14.04, and UGENE 1.20. Unlike earlier versions the new version gives error with external tools:

[ERROR][16:13] Trying to recover from error: PhyTree Generator is NULL at src/phyltree/CreatePhyTreeDialogController.cpp:122
[ERROR][16:14] Task {Calculating Phylogenetic Tree} finished with error: Subtask {PhyML tree calculation} is failed: PhyML Maximum Likelihood tool exited with code 1

[ERROR][16:37] Trying to recover from error: PhyTree Generator is NULL at src/phyltree/CreatePhyTreeDialogController.cpp:122
[ERROR][16:37] Task {Calculating Phylogenetic Tree} finished with error: Subtask {MrBayes tree calculation} is failed: MrBayes tool exited with code 1

Please fix this issue. Old version on my Mac works fine.

Bade
 
IP Logged
 
Reply #1 - Feb 11th, 2016 at 4:11pm

German   Offline
Full Member

Posts: 118
***
 
Hello, AK.

There are 2 different problems with your UGENE installation:
1. When you open a Build Tree dialog, it is almost empty and there is a error in log "PhyTree Generator is NULL". We've got to reproduce it and it will be fixed in the upcoming UGENE 1.21. Follow the progress here.
2. MrBayes and PhyML don't work, they finish with an error.

How to fix problem 1:
As I understood you have installed UGENE from PPA. Am I right? If yes, it will be better if you install the non-free UGENE plugins (PLHYLIP is one of them) with the following command:
sudo apt-get install ugene-non-free
PHYLIP is distributed with another license that's why it is not included into the main UGENE package.

How to fix problem 2:
I can't answer it now, because I can't reproduce it. Could you help me with it?
Currently I need to know what MrBayes and PhyML versions you use. You can check it in UGENE:
a. Click the menu Settings -> Preferences.
b. Click the "External Tools" section.
c. Find MrBayes and click it.
d. Check its version in the additional information block.
Repeat c and d for PhyML.
 

mrbayes.png (153 KB | 346 )
mrbayes.png
IP Logged
 
Reply #2 - Feb 11th, 2016 at 11:20pm

AK   Offline
YaBB Newbies

Posts: 14
*
 
Thanks for your reply. 2nd issue was because of some problem with Clustal Omega output, it seems incompatible with PhyML and MrBAYES, at least for the sequences that I have. I have even tested using command line version of PhyML and it gives an error related to "negative taxa".

Both PhyML and MyBAYES work well with ClustalW output of same sequences. Sorry for bothering you.

Atul

 
IP Logged
 
Reply #3 - Feb 12th, 2016 at 11:33am

German   Offline
Full Member

Posts: 118
***
 
Very nice! Thank you for the reported problem. By the way, it is already fixed. UGENE 1.21 is planned to be released on the 17th of February.
 
IP Logged
 
Page Index Toggle Pages: 1