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[ADDITION] GA Branch batch files (Read 4893 times)
Sergei
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[ADDITION] GA Branch batch files
Nov 21st, 2006 at 4:00pm
 
Greetings,

Just posted two HyPhy batch files needed to run and process a GA Branch analysis for temporal variation in selective pressure (along branches) on your local cluster. The archive with the files and an extensive README are linked from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

Cheers,
Sergei
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krish
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Re: [ADDITION] GA Branch batch files
Reply #1 - Nov 30th, 2006 at 6:52pm
 
Dear All,

I have been trying to run the GA branch specific detection locally.
I started the batch file ModelSelectorBranchLocal.bf and then it asks for my datafile. But when I input my file.
IT give out an error:

GABranchspecific#189EA3:_BMS_Aux.ibf could not be opened by fscanf.
Current BL Command:Read the following data "_BMS_Aux.ibf":Raw into sampleCount; Current operation/job has been terminated.

Any help would be greatly appretiated.

Thanks,
Vijay
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Sergei
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Re: [ADDITION] GA Branch batch files
Reply #2 - Nov 30th, 2006 at 8:18pm
 
Dear Vijay,

Please make sure you are running the latest version of HyPhy and that the _BMS_Aux.ibf file is in the same directory. A sufficiently recent version of HyPhy will also print out a path stack to the console if it can't locate a file that is required. If the problem persists, let me know.

Cheers,
Sergei
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tlefebure
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Re: [ADDITION] GA Branch batch files
Reply #3 - Dec 5th, 2006 at 7:47am
 
Dear Sergei,

I have a similar problem. I use, on a cluster, the version:
Code:
/HYPHY 0.9920060914beta(MPI) for Linux on x86_64\
 



GARD run great, but not the GA-branch.

After I copied the full HYPHY folder to all the nodes (which was not necessary with GARD), and run hyphy with the following command:
Code:
$MPIDIR/mpirun -np $PROCS -machinefile machines $HYPHY BASEPATH=$HYPHYDIR /state/partition1/ModelSelectorBranchLocal.bf < $ANSW >& output 



with
Code:
set DATA=pbp1a.phy
set ANSW=answers
set MPIDIR=/opt/mpich/gnu/bin
set HYPHY=/state/partition1/HYPHY_Source/HYPHYMPI
set HYPHYDIR=/state/partition1/HYPHY_Source/
 



I obtain the following error:
Code:
[tnl7@biosim 1a]$ cat output


				+-------------------+
				|Choose Genetic Code|
				+-------------------+


	  (1):Universal code. (Genebank transl_table=1).
	  (2):Vertebrate mitochondrial DNA code. (Genebank transl_table=2).
	  (3):Yeast mitochondrial DNA code. (Genebank transl_table=3).
	  (4):Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).
	  (5):Invertebrate mitochondrial DNA code. (Genebank transl_table=5).
	  (6):Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).
	  (7):Echinoderm mitochondrial DNA code. (Genebank transl_table=9).
	  (8):Euplotid Nuclear code. (Genebank transl_table=10).
	  (9):Alternative Yeast Nuclear code. (Genebank transl_table=12).
	  (10):Ascidian mitochondrial DNA code. (Genebank transl_table=13).
	  (11):Flatworm mitochondrial DNA code. (Genebank transl_table=14).
	  (12):Blepharisma Nuclear code. (Genebank transl_table=15).

 Please choose an option (or press q to cancel selection):
(/state/partition1/) Codon file to analyze:Error:MPI Node:0
/state/partition1/_BMS_Aux.ibf could not be opened for reading by fscanf. Path stack: {/state/partition1/,/state/partition1/}
Current BL Command:Read the following data from "_BMS_Aux.ibf":Raw into sampleCount;
p0_31098:  p4_error: interrupt SIGx 



What is the "_BMS_Aux.ibf" file?
Is my HYPHY out of date?

Thank you Sergei...

-Tristan
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Sergei
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Re: [ADDITION] GA Branch batch files
Reply #4 - Dec 5th, 2006 at 8:15am
 
Dear Tristan and Vijay,

My bad! The archive was missing two files needed for the execution. Please download the new one I just put up (from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login) and try again.

Best,
Sergei
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tlefebure
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Re: [ADDITION] GA Branch batch files
Reply #5 - Dec 5th, 2006 at 8:47am
 
Yes, it runs now with the additional ibf files.
Cheers,
-Tristan
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tlefebure
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Re: [ADDITION] GA Branch batch files
Reply #6 - Sep 25th, 2010 at 2:16pm
 
Hi Sergei,

In the archive Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login, I can't find the file lysozyme.nex_ga_branch.out that is mentioned in the documentation (README.pdf, page 3, first paragrah). Would it be possible to get it? Also, it would be great to know how long it takes you on your cluster for this data (with the 17 processors). I am running a 80taxa x 600bp, and it seems to be very slow. I wonder if I have a problem with my MPI cluster, or if there is too many taxa...

Thanks!

--Tristan
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Sergei
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Re: [ADDITION] GA Branch batch files
Reply #7 - Sep 27th, 2010 at 2:57pm
 
Hi Tristan,

tlefebure wrote on Sep 25th, 2010 at 2:16pm:
Hi Sergei,

In the archive Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login, I can't find the file lysozyme.nex_ga_branch.out that is mentioned in the documentation (README.pdf, page 3, first paragrah). Would it be possible to get it? Also, it would be great to know how long it takes you on your cluster for this data (with the 17 processors). I am running a 80taxa x 600bp, and it seems to be very slow. I wonder if I have a problem with my MPI cluster, or if there is too many taxa...


If you run the GA on the lysozyme.nex file it will generate lysozyme.nex_ga_branch.out in the process. This analysis should take < 30 minutes on a 17 processor cluster. 80 taxa x 600 bp should take no more than a day on your system, unless you are using a really old version of HyPhy.

HTH,
Sergei
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Division of Biomedical Informatics
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tlefebure
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Re: [ADDITION] GA Branch batch files
Reply #8 - Sep 30th, 2010 at 2:06am
 
Thanks Sergei,
I found the problem: the data set and tree have to be copied to all the nodes, not just the head node... Works much faster now!
--Tristan
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