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Bad Binary Operator Placement: (Read 1627 times)
DavidW
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Bad Binary Operator Placement:
Nov 28th, 2011 at 7:30am
 
Hi

On running a GARD analysis, I get an error:

Bad Binary Operator Placement:+?siteDifferenceCount

which crashes the analysis very early on (it definitely starts and accepts the commands I give it). I found a wiki entry about something similar: hyphywiki/index.php/Trouble:Bad_Binary_Operator_Placement
but it doesn't seem to be exactly the same issue and there doesn't seem to be a solution . .

Has anyone solved something similar?

Thanks.

David
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Sergei
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Re: Bad Binary Operator Placement:
Reply #1 - Nov 28th, 2011 at 2:20pm
 
Hi David,

Are you running the most recent version of HyPhy (should be version 2.10xxxx?)
The error you are seeing indicates to me that you may be running a version of HyPhy which does not understand the '+=' operator added about 9 months ago.

Sergei
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DavidW
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Re: Bad Binary Operator Placement:
Reply #2 - Nov 28th, 2011 at 4:33pm
 
Thanks Sergei

That is almost certainly the case. I shall send a request to my cluster administrator.

David
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Sergei
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Re: Bad Binary Operator Placement:
Reply #3 - Nov 28th, 2011 at 4:34pm
 
Hi David,

You can also install HyPhy in your home directory and bypass the admin to speed things up.

Sergei
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DavidW
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Re: Bad Binary Operator Placement:
Reply #4 - Nov 29th, 2011 at 6:07pm
 
Part of the problem was that I was getting the source code with:

svn co XXXXXXXdatam0nk3y.org/svn/hyphy  (!) (censored with XXX so I can post the link)

It seems this could be obsolete now (2.00xxx) but will still give out source code if asked.

The other problem was that I was feeding it the wrong file   Roll Eyes

The latest github code (2.1020111129beta(MP) for Linux on x86_64) seems to be working.

. . . actually, this time GARDProcessor.bf fitted a single-tree, multiple partition model, printed 30 trees to the screen but then quit with:

Fitting a mutilple tree, multiple partition model
Error:
Unbalanced Parentheses in Expression:]?

Function call stack
1 : Build Tree tree_1 from string ]
-------
2 : ExecuteCommands in string "Tree tree_"+pccounter+" = "+partLines[pccounter*2+3]+";" using basepath /home/play/Work/Apps/hyphy/lib/hyphy/TemplateBatchFiles/.
-------
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Sergei
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Re: Bad Binary Operator Placement:
Reply #5 - Nov 30th, 2011 at 1:08pm
 
Hi David,

Please be sure to supply the .splits file when prompted -- the error you see is suggesting to me that HyPhy is trying to read the NEXUS file as a list of Newick strings and coordinate ranges (which is what is in the .splits file). Take a look at page 7 in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for more details.

Sergei
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