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Problem with REL? (Read 2546 times)
matty
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Problem with REL?
Jun 6th, 2007 at 1:50pm
 
I started a REL analysis this morning, and usually it does not take this long to finish.  I was actually expecting this one to run really fast due to the limited number of codons I have.  However, it says it is still in the job queue. 

My results page is also blank (except for the beloved monkey sipping on his java):
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Just wondering if you knew what was up, or if its just my lack of patience.  Thanks.
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Sergei
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Datamonkeys are forever...

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Re: Problem with REL?
Reply #1 - Jun 6th, 2007 at 2:06pm
 
Dear matty,

This job threw an exception I have not seen yet (it was not being run properly). Let me check and see what is going on.

Cheers,
Sergei
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Division of Infectious Diseases
Division of Biomedical Informatics
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University of California San Diego
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Sergei
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Re: Problem with REL?
Reply #2 - Jun 6th, 2007 at 5:15pm
 
Dear matty,

The tree included in your NEXUS file had one too many opening parentheses (at the beginning). HyPhy accepted this tree (but it should have rejected it, I need to tighten error checking), and created a phantom node (i.e. a branch with a dummy interior node). That in turn led to issues with the server side of datamonkey.org.

Check Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for the results using your file but with the tree string corrected to balance the parentheses.

Cheers,
Sergei
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Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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matty
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Re: Problem with REL?
Reply #3 - Jun 7th, 2007 at 10:02am
 
Thanks for your help!

Matty
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