Dear Datamonkeys,

I am new to HyPhy, so maybe my questions are easy and already addressed elsewhere.

I want to run GARD on many (~5000) different alignments.
I managed to install HYPHYMPI and get GARD.bf running, now I need to get it automated. Thus I was wondering if it is possible to create an option file where I will provide input file name, model of evolution, rate across sites variation (I would use General Discrete with 4 rate categories) and output file name. If it is possible, then how do I do that?

Another questions are:
Is it possible to run GARD locally on protein alignments (that is what I would prefer to do)?
What are the codes for different evolutionary models? So far I know only 010010 (stands for HKY85).

Thanks a lot!

Hi Sergei,

Thank you very much for being so very fast and helpful!

To the 1st point.
I run GARD.bf in terminal like that:
$mpirun -np 4 HYPHYMPI GARD.bf

then I give input file name (for instance, gr_1000_al_dna1)
code for a model (for instance, 010010)
choose rate across sites variation (2, general discrete)
choose number of bins (4)
specify output file (for instance, gr_1000_al_dna1_gard_res2)
GARD runs just fine.

Now I create a file (run_gard) with the next content:
inputRedirect = {};
inputRedirect[’’01’’]=’’./gr_1000_al_dna1’’;
inputRedirect[’’02’’]=’’010010’’;
inputRedirect[’’03’’]=’’2’’;
inputRedirect[’’05’’]=’’4’’;
inputRedirect[’’06’’]=’’./gr_1000_al_dna1_gard_res2’’;
ExecuteAFile (’’./GARD.bf’’, inputRedirect);


Now I am trying to execute it in terminal like this and here is what I am getting:
$mpirun -np 4 HYPHYMPI run_gard
Error:MPI Node:0
Bad symbols in expression inputRedirect[????’01’’]=’’./gr_1000_al_dna1’’
Current BL Command:inputRedirect[’’01’’]=’’./gr_1000_al_dna1’’

Am I missing something obvious here?
Is it a problem of mpi or of hyphy?




To the 2nd point.
If I understand correctly, in the 6 symbol string, same numbers denote parameters of the model (corresponding substitution rates) which have to have the same values estimated from the data. Thus, if I want to specify general time reversible model (I understand the danger of using this model) I will put 01234?
Is it correct?


Thank you very much,
Olga.

Yes, it did work! At least started. However, it still does not accept all the options:

This is my current control file:
inputRedirect = {};
inputRedirect["01"]="./gr_1000_al_dna1";
inputRedirect["02"]="012345";
inputRedirect["03"]="2";
inputRedirect["05"]="4";
inputRedirect["06"]="./gr_1000_al_dna1_gard_res2";
ExecuteAFile ("./GARD.bf", inputRedirect);


This is what I am getting when trying to run hyphy:
[okamneva@sheep4 HyPhy]$ mpirun -np 4 HYPHYMPI run_gard
Initialized GARD on 4 MPI nodes.
Population size is 6 models

Please enter a 6 character model designation (e.g:010010 defines HKY85):Error:MPI Node:0
Not a valid option: '2' passed to Choice List 'Rate variation options' using redirected stdin input
Current BL Command:Choice List for Rate variation options with choice list:SKIP_NONE. Store result in rvChoice
[okamneva@sheep4 HyPhy]$



Seems like I need to pass choice from the list somehow differently then just a string.


Thanks for any suggestions,
Olga.

does not seem to work ether.




[okamneva@sheep4 HyPhy]$ more run_gard
inputRedirect = {};
inputRedirect["00"]="./gr_1000_al_dna1";
inputRedirect["01"]="012345";
inputRedirect["02"]="2";
inputRedirect["03"]="4";
inputRedirect["04"]="./gr_1000_al_dna1_gard_res2";
ExecuteAFile ("./GARD.bf", inputRedirect);
[okamneva@sheep4 HyPhy]$ mpirun -np 4 HYPHYMPI run_gard
Initialized GARD on 4 MPI nodes.
Population size is 6 models

Please enter a 6 character model designation (e.g:010010 defines HKY85):Error:MPI Node:0
Not a valid option: '2' passed to Choice List 'Rate variation options' using redirected stdin input
Current BL Command:Choice List for Rate variation options with choice list:SKIP_NONE. Store result in rvChoice
[okamneva@sheep4 HyPhy]$

So in your example, try replacing "2" with "Beta-Gamma".

Great, glad it worked!  But please don't call it a "control file" - that's so PAML. 
We much prefer "HBL script".

Hi Olga,

The error you are seeing is unusual -- it occurs when HyPhy can't initialize model parameters to sensible values BEFORE optimization.
This typically happens when something is not appropriately reset between consecutive runs. Could you possible attach one of the 28 problematic files so that I can troubleshoot the bug?

SBP is implemented in 'SingleBreakpointRecomb.bf', which is a standard analysis under the recombination rubrik. You can find the file itself inside the 'TemplateBatchFiles' directory.

Sergei