HyPhy message board - Questions About GARD

Sundy

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Questions About GARD
Feb 12^th, 2009 at 7:03am

Dear Sergei,

Recently, when I run HyPhy to do KH test for GARD result, I always got the following problem:

Operation MAccess is not defined for 0
Current BL command: jvec[1][k]=vec2[k] Current task has been terminated. Would you like to see the remaining error messages, if there are any?

Could you please help me tell me the reason? Thank you very much.

My job on Datamonky is: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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and the attached file is what I need test.
Thank you very much

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Sundy

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Re: Questions About GARD
Reply #1 - Feb 12^th, 2009 at 9:21am

Dear Sergei,

I got another problem as following when I run GARD

This analysis was stopped before convergence, because the CPU time limit per job was reached. The reported results may, therefore be incomplete, as there may be more breakpoints, for example. Consider reducing the size of the alignment, either by removing sequences or selecting shorted sequence regions, or choosing a simpler model (no rate variation etc).

My dataset contains 10 sequences (3765bp). I tried simpler model (no rate variation etc), but it still give me this information.
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could you please tell me how to fix this problem?

Thank you very much!!

Sundy

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Sergei

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Re: Questions About GARD
Reply #2 - Feb 12^th, 2009 at 2:15pm

Dear Sundy,

Because there are a number of people at any given time that are trying to use Datamonkey (which is a free resource), we must limit the duration that any individual job takes on the cluster -- in this case to one hour. GARD files are a part of the HyPhy distribution and if you have access to a computer cluster you can run the analysis for as long as it takes to finish.

That said, your analysis is still useful - there is clearly a very strong recombination signal in your alignment. You could try breaking it up into smaller fragments (e.g. the first 1485 nucleotides and the remainder) and run them as two separate jobs.

HTH,
Sergei

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Sundy

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Re: Questions About GARD
Reply #3 - Feb 12^th, 2009 at 2:42pm

Dear Sergei,

Thank you so much. I got it.

About the first question as following, I still can not fix it, and I met this problem several times. Could you please have a look of it also.

Thank you!!

Sundy

Sundy wrote on Feb 12^th, 2009 at 7:03am:

Dear Sergei,

Recently, when I run HyPhy to do KH test for GARD result, I always got the following problem:

Operation MAccess is not defined for 0
Current BL command: jvec[1][k]=vec2[k] Current task has been terminated. Would you like to see the remaining error messages, if there are any?

Could you please help me tell me the reason? Thank you very much.

My job on Datamonky is: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login
and the attached file is what I need test.
Thank you very much

Back to top

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