Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
NJtree.TG is already been used (Read 5308 times)
Antonio
Guest


NJtree.TG is already been used
Oct 25th, 2005 at 3:16am
 
hi, I am getting an strange crash since I am doing something I think I done before without problems  ???.

Whith MoleculaClock.bf or whenever I open a tree file I get a message as "NJtree.TG is already being used- please rename one of these two variables". I get the same message when I compute a NJtree and try to store it programatically, that is: the same message as before, plus "Current BL comman:d Build NJTree from String mytreeString...

Sincerely,
Antonio
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: NJtree.TG is already been used
Reply #1 - Oct 25th, 2005 at 7:10am
 
Dear Antonio,

Check for '.' (or other non-alphanumerics) in sequence names and replace them with underscores. If that is not the issue, then I may have to see the data file to replicate the error.

Cheers,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
Antonio
Guest


Re: NJtree.TG is already been used
Reply #2 - Oct 25th, 2005 at 8:11am
 
Thankyou very much, it was my fault, there was one file with bad format somewhere.
,
antonio
Back to top
 
 
IP Logged
 
Sarah
Guest


Re: NJtree.TG is already been used
Reply #3 - Aug 29th, 2006 at 11:08am
 
I'm having a similar problem, but I can't find an error in my tree file. Does HyPhy not tolerate prespecified branch lengths?

Thanks for the help.
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: NJtree.TG is already been used
Reply #4 - Aug 29th, 2006 at 11:23am
 
Dear Sarah,

HyPhy will read branch lengths, provided they are properly formed numbers. I'll be happy to take a look at your tree (just e-mail it to me as an attachment) and see if I can find what the problem is.

Cheers,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
Sarah
Guest


Re: NJtree.TG is already been used
Reply #5 - Aug 30th, 2006 at 7:03am
 
<doh> Not enough coffee yesterday--I think the problem might be the bootstrap values in all my Newick files. HyPhy doesn't tolerate them, right?

Thank you for the help.

Sarah
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: NJtree.TG is already been used
Reply #6 - Aug 30th, 2006 at 7:33am
 
Dear Sarah,

Quote:
<doh> Not enough coffee yesterday--I think the problem might be the bootstrap values in all my Newick files. HyPhy doesn't tolerate them, right?


Depends on how they are specified. Could you paste in a short fragment of the tree?

Cheers,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
Sarah
Guest


Re: NJtree.TG is already been used
Reply #7 - Aug 30th, 2006 at 7:59am
 
Here's a small fragment I copied directly from the end--the parentheses don't match:

(5HK6869:0.00517100,4HK6868:0.01945300)36:0.00108000)22:0.00000000,13HK6871:0.01
482200)62:0.00206400,(6HK6869:0.00103300,((9HK6870:0.00312700,8HK6870:0.00418200
)69:0.00102000,7HK6869:0.00103400)54:0.00103400)71:0.00206900)94:0.00000000,3HK6
868:0.00000000,2HK6868:0.00000000);

The tree is the output from a PHYML run with 100 bootstraps. My sequence names are all alphanumerics <=10 characters long.

Sarah

Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: NJtree.TG is already been used
Reply #8 - Aug 30th, 2006 at 8:14am
 
Dear Sarah,

Sequence names and branch lengths are fine, but HyPhy will interpret bootstrap support for internal branches as branch names (e.g. ...13HK6871:0.01482200)62 will give the parent of 13HK6871 the name '62'). If any two internal branches have the same BS support, you'll run into the 'duplicate name' issue.

Cheers,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged
 
Sarah
Guest


Re: NJtree.TG is already been used
Reply #9 - Aug 30th, 2006 at 8:16am
 
Thank you!

I will remove the bootstrap values, then (assuming there's no way to tag them so HyPhy read/ignores them).

I really appreciate the help.

Sarah
Back to top
 
 
IP Logged