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error messages in directionalREL.bf (Read 9343 times)
Kohei
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error messages in directionalREL.bf
Jun 25th, 2010 at 12:21am
 
Thank you for creating HyPhy.
I am trying directionalREL.bf with Win7 x64 and WinXP x32 platforms and
faced error messages as follows,

after > Reload/New (New analysis) > (file specification) > Substitution Model (any model in the list).
------------
"Problem occurred in line:global freqParam_4=vf[k]
Call stack
4 : global freqPram_4=vf[k]
3 : ExcuteCommands in string "global freqParam_"+k+"=vf[k]; freqParam_"+k+":<1;" reading input from
x:\HYPHY2.0\TemplateBatchFiles\TemplateModels\
2 : ExecuteAFile fro Current Task has been terminated. Would you like to see the remaining error messages, if there are any?"

"Problem occurred in line:global freqParam_4=vf[k]
Call stack
4 : global freqPram_4=vf[k]
3 : ExcuteCommands in string "global freqParam_"+k+"=vf[k]; freqParam_"+k+":<1;" reading input from
x:\HYPHY2.0\TemplateBatchFiles\TemplateModels\
2 : ExecuteAFile f Current Task has been terminated. Would you like to see the remaining error messages, if there are any?"

"Problem occurred in line:promptModel(0)
Call stack
1 : promptModel(0)
Current Task has been terminated. Would you like to see the remaining error messages, if there are any?
------------
Could you kindly confirm the same problem is reproduced in your Windows platform? Cry
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Sergei
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Re: error messages in directionalREL.bf
Reply #1 - Jun 25th, 2010 at 5:53am
 
Dear Kohei,

Thanks for reporting this error message. I confirmed that it is generated if you provide a nucleotide alignment as input to DirectionalREL.bf
The analysis expects a protein (i.e. 20 residues, not 4) alignment, but does not report the error in an informative way. I will fix the file to specifically check for whether or not a protein alignment has been submitted. In the meantime, please try to run DirectionalREL.bf on a protein alignment and tell me if it works on your system.

Sergei
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Kohei
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Re: error messages in directionalREL.bf
Reply #2 - Jun 26th, 2010 at 6:28am
 
Dear Sergei,

Thank you for the prompt reply!
Now I succeeded to start the calculation (now it's running).
I will check the result when it's finished.

Kohei
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Kohei
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Re: error messages in directionalREL.bf
Reply #3 - Jun 27th, 2010 at 5:52pm
 
Sorry again, but after 37 hours calculation with Core 2 Quad Q9650 CPU (3.00 GHz) machine, another error message appeared.
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Kohei
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Re: error messages in directionalREL.bf
Reply #4 - Jun 27th, 2010 at 5:54pm
 
This is another message,
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Kohei
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Re: error messages in directionalREL.bf
Reply #5 - Jun 27th, 2010 at 5:57pm
 
and this is HYPHY Console Window.
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Kohei
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Re: error messages in directionalREL.bf
Reply #6 - Jun 27th, 2010 at 6:06pm
 
and this is the data file analyzed. Did I have to remove questionable sites (?) and sequences with too many blanks?
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Re: error messages in directionalREL.bf
Reply #7 - Jun 28th, 2010 at 9:55am
 
This looks like an execution path problem.  Where is your HYPHY distro on your hard drive?  Where are the DREL files?
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Kohei
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Re: error messages in directionalREL.bf
Reply #8 - Jun 28th, 2010 at 10:04am
 
Thank you for the response.
As in the error messages, the HYPHY distributions are under K:\MyDocuments\Downloads\HYPHY2.0

. What is "DREL files"? If it is the data file being analyzed, K:\MyDocuments\Documents\n中込研\YenProject\20100408~HyPhy解析\20100625DirectionalEvolutionProteinSequences(DEPS)を試す

oh...problem in the folder name?
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Re: error messages in directionalREL.bf
Reply #9 - Jun 28th, 2010 at 10:19am
 
Based on the console output, it looks like the path is okay.  Can you check the folder HYPHY_BASE_DIRECTORY/ChartAddins/DistributionAddIns/Includes to make sure that the posteriors.ibf include file is present?

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Re: error messages in directionalREL.bf
Reply #10 - Jun 28th, 2010 at 10:21am
 
Oh, and DREL is another name for DEPS. 
Ambiguous and partial sequences should be OK.
I'm wondering if this is a locale issue (i.e., directory separators).  Sergei?
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Kohei
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Re: error messages in directionalREL.bf
Reply #11 - Jun 28th, 2010 at 10:34am
 
I found posteriors.ibf under K:\MyDocuments\Downloads\HyPhy1.0\HYPHY_Win32\ChartAddIns\DistributionAddIns\Inc
ludes

but the issue is I found no posteriors.ibf under K:\MyDocuments\Downloads\HYPHY2.0
, which I am using. Is this the reason?
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Re: error messages in directionalREL.bf
Reply #12 - Jun 28th, 2010 at 10:48am
 
Hi Kohei,

The 2.0 windows distribution was missing the ChartAddIns directory. I have just rebuild it: please download it from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login and see if this fixes the missing file issue. Try running a small protein file first to confirm that everything is in order.

Sergei
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Kohei
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Re: error messages in directionalREL.bf
Reply #13 - Jun 28th, 2010 at 11:00am
 
Thank you for the quick fix. I am now re-running the analysis and will inform you the results.
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Kohei
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Re: error messages in directionalREL.bf
Reply #14 - Jul 1st, 2010 at 8:07pm
 
Thank you for your help.
First, DirectionalREL.bf was run with JTT model for the same alignment, and the calculation finished within 5 hours. Amino acid sites 51, 120, 157, and 309 were selected (please see attached file). However, I found so many N/A in a resulted xxx_AA_bysite.csv file and I doubted whether the settings were adequate. Are there any documentation about DirectionalREL.bf in addition to Kosakovsky Pond et al. (2008) Molecular Biology and Evolution 25:1809-1824?
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