HyPhy message board - Error: Invalid Matrix Index [0][0] in a 0 by 1 mat

jose

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Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Feb 22^nd, 2010 at 9:43am

Hello,
I get the error shown below when trying to run dNdSRateAnalysis.bf for only the Constant model:

Error:
Invalid Matrix Index [0][0] in a 0 by 1 matrix.
Call stack
3 : rateStrMx[0]="RN_1"
2 : ExecuteAFile from file "2RatesAnalyses/discreteGenerator.bf" using basepath /home/jose/hyphy/HYPHY/TemplateBatchFiles/.
1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"dNdSRateAnalysis.
bf" using basepath /home/jose/. reading input from inputRedirect

I use version 2.0. When i run all the Rate Variation Models (option "Run all") it works. But i would prefer to run only constant for speed reasons.

Thanks.

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Sergei

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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #1 - Feb 22^nd, 2010 at 12:17pm

Hi Jose,

There was a bug in the HyPhy dNdSRateAnalysis.bf code; I updated the file on SVN; you can download the replacement and drop it into TemplateBatchFiles (make sure the file is REPLACED; the default download will add .txt to the name of the file - remove that).

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Note, that you also need to modify your wrapper file, because HyPhy will not prompt for any of the distributional options for the constant rate model.

Sergei

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jose

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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #2 - Feb 23^rd, 2010 at 7:39am

Hi Sergei,

Yes now it works. I will bear in mind that link. I have removed the distributional options also in the wrapper file.

I would like to get the w rates, however I only get the synRates (but not the nonSynRates) in the output.Constant.fit file:

givenTree.Node2.synRate=0.2498200842255637;
givenTree.FBgn0224725_Dwil.synRate=1.748285438938617;
givenTree.FBgn0081989_Dpse.synRate=0.8752885212323878;
...

Moreover, is it possible to run dNdSRateAnalysis.bf with "local" branch rates? I think it performs only global analysis. I have tried with AnalyzeCodonData.bf but I can´t get that. I would like to do in command line the same I do in HYPHY GUI when I do:

File>Open>Open Data File > partition > tree > subs model > parameters (local) > build function > optimize function

which returns synRate and nonSynRates for each branch.

Thanks, once again Embarrassed

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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #3 - Feb 23^rd, 2010 at 9:44am

Hi Jose,

You can get the "local" model from AnalyzeCodonData.bf if you select "Local" (instead of "Global") from the model parameter dialog, e.g. for MG94Custom.

Cheers,
Sergei

Code:

fileName = "/Users/sergei/hyphy/TestSuite/data/HIVenvSweden.seq";

localCodon = {"0" : "Universal",
			  "1" : fileName,
			  "2" : "MG94CUSTOM",
			  "3" : "Local",
			  "4" : "012345",
			  "5" : "y"};

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "AnalyzeCodonData.bf",
			  localCodon);

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jose YaBB Newbies Offline Feed your monkey! Posts: 7	Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat Reply #4 - Feb 23^rd, 2010 at 1:41pm Thanks it works ... So now how can I get synRate and nonsynRates? In the GUI I would do: Analyses> Results > view results > filename_LF > Parameters + values Do I need to add some code into AnalyzeCodonData.bf? cheers, jose
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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #5 - Feb 23^rd, 2010 at 3:28pm

Hi Jose,

You can access all parameter names programmatically; in this case the standard analysis has 'preset' names for the tree variable, so it can be hard-coded.

Try:

Code:

fileName = "/Users/sergei/hyphy/TestSuite/data/HIVenvSweden.seq";

localCodon = {"0" : "Universal",
			  "1" : fileName,
			  "2" : "MG94CUSTOM",
			  "3" : "Local",
			  "4" : "012345",
			  "5" : "y"};

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "AnalyzeCodonData.bf",
			  localCodon);

branchNames = BranchName (givenTree, -1);

synName    := "givenTree." + branchNames[branchIndex] + ".synRate";
nonSynName := "givenTree." + branchNames[branchIndex] + ".nonSynRate";

fprintf (stdout, "\n");

for (branchIndex = 0; branchIndex < Columns (branchNames); branchIndex = branchIndex + 1)
{
	fprintf (stdout, synName, " = ", getParameterValue (synName), "\n");
	fprintf (stdout, nonSynName, " = ", getParameterValue (nonSynName), "\n");
}

function getParameterValue (parameterName)
{
	ExecuteCommands ("pv=" + parameterName);
	return pv;
}

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jose

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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #6 - Feb 24^th, 2010 at 4:27am

Awesome!
The synRates (and nonSynRates) are arbitrary parameters of the model, do they have units?. Can I compare directly local synRates among lineages and genes?

How can I get in batch language the syn and non-syn trees? (In GUI: analysis> results > syn and non-syn trees).

e.g:

Total nucleotide sites :4191
Total sense codon sites:4050.8
Synonymous sites :996.426
Nonsynonymous sites :3054.38

E[Syn subs/nucleotide site] tree:
…
E[Non-syn subs/nucleotide site] tree:
…

dS tree:
…

dN tree:
...

Thanks very much. (hopefully) me done with this thread Lips Sealed

...

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Re: Error: Invalid Matrix Index [0][0] in a 0 by 1 mat
Reply #7 - Feb 24^th, 2010 at 10:45am

Hi Jose,

You can just call the appropriate dN/dS calculator from your script, as in

Code:

fileName = "/Users/sergei/hyphy/TestSuite/data/HIVenvSweden.seq";

localCodon = {"0" : "Universal",
			  "1" : fileName,
			  "2" : "MG94CUSTOM",
			  "3" : "Local",
			  "4" : "012345",
			  "5" : "y"};

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "AnalyzeCodonData.bf",
			  localCodon);

branchNames = BranchName (givenTree, -1);

synName    := "givenTree." + branchNames[branchIndex] + ".synRate";
nonSynName := "givenTree." + branchNames[branchIndex] + ".nonSynRate";

fprintf (stdout, "\n");

for (branchIndex = 0; branchIndex < Columns (branchNames); branchIndex = branchIndex + 1)
{
	fprintf (stdout, synName, " = ", getParameterValue (synName), "\n");
	fprintf (stdout, nonSynName, " = ", getParameterValue (nonSynName), "\n");
}

dNdSOptions = {"0":"Display"};

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "post_sns.bf",
			  dNdSOptions);


function getParameterValue (parameterName)
{
	ExecuteCommands ("pv=" + parameterName);
	return pv;
}

Sergei

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