search

veg / hyphy

HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
Other
210 stars 69 forks source link

Is GARD running? #451

Closed ATVincent closed 8 years ago

ATVincent commented 8 years ago

Hi,

I am trying to run GARD on several alignments before running PARRIS. I launched GARD on a test alignment file as follows:

avincent@Grumpy:~/Desktop/SOFTWARE/hyphy-2.2.4$

mpirun -np 8 ./HYPHYMPI

   /HYPHY 2.220160718beta(MPI) for Linux on x86_64\

***** TYPES OF STANDARD ANALYSES *****

(1) Basic Analyses
(2) Codon Selection Analyses
(3) Compartmentalization
(4) Data File Tools
(5) Miscellaneous
(6) Model Comparison
(7) Kernel Analysis Tools
(8) Molecular Clock
(9) Phylogeny Reconstruction
(10) Positive Selection
(11) Recombination
(12) Selection/Recombination
(13) Relative Rate
(14) Relative Ratio
(15) Substitution Rates

11 Please select type of analyses you want to list (or press ENTER to process custom batch file):

***** FILES IN 'Recombination' ***** 

(1) Screen an alignment using GARD (requires an MPI environment).
(2) Process GARD results.
(3) A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo].
(4) Search an alignment for a single breakpoint.
(5) Plot genetic distances (similarity) of one sequence against all others in an alignment, using a sliding window. Optionally, determine NJ-based clustering and bootstrap support in every window. This is a HyPhy adaptation of the excellent (but Windows only tool) SimPlot (and/or VarPlot) written by Stuart Ray (http://sray.med.som.jhmi.edu/SCRoftware/simplot/)

1 Please select the file you want to use (or press ENTER to return to the list of analysis types):Initialized GARD on 8 MPI nodes. Population size is 14 models

seq.fas /home/avincent/Desktop/SOFTWARE/hyphy-2.2.4/installation_final/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::

It seems to calculate on 8 threads, but nothing happens. My test file is simply a small alignment containing 18 taxa. Do I miss something? Thank you!

stevenweaver commented 8 years ago

Hello @antony03,

After supplying your nucleotide file to screen, you should receive the following prompt: Please enter a 6 character model designation (e.g:010010 defines HKY85):

A known issue at the moment is that some users have to enter the path to the nucleotide file twice before the program will continue. Can you please try that?

Best, Steven

ATVincent commented 8 years ago

Thank you, it works perfectly if I enter the file name twice.

Sincerely,

Antony