Ms-Teaching

Category

Bioinformatics

Program On

Teaching

Version

20140304 (latest recorded change was made on Mar. 4, 2014.)

Author / Distributor

Richard Hudson

Description

Program to generates samples of gametes. For more information, please see https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13 (and the msdoc.pdf file there).

Running Program

• Version 20140304 is installed at /usr/local/apps/gb/ms/20140304

To use this version, please load the module with

ml ms/20140304

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_ms
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=2gb
#SBATCH --time=08:00:00
#SBATCH --output=ms.%j.out
#SBATCH --error=ms.%j.err

cd $SLURM_SUBMIT_DIR
ml ms/20140304
ms [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

The manual msdoc.pdf is available in the directory /usr/local/apps/gb/ms/20140304/ms

ml ms/20140304

ms --help
Too few command line arguments
usage: ms nsam howmany 
  Options: 
	 -t theta   (this option and/or the next must be used. Theta = 4*N0*u )
	 -s segsites   ( fixed number of segregating sites)
	 -T          (Output gene tree.)
	 -F minfreq     Output only sites with freq of minor allele >= minfreq.
	 -r rho nsites     (rho here is 4Nc)
		 -c f track_len   (f = ratio of conversion rate to rec rate. tracklen is mean length.) 
			 if rho = 0.,  f = 4*N0*g, with g the gene conversion rate.
	 -G alpha  ( N(t) = N0*exp(-alpha*t) .  alpha = -log(Np/Nr)/t
	 -I npop n1 n2 ... [mig_rate] (all elements of mig matrix set to mig_rate/(npop-1) 
		 -m i j m_ij    (i,j-th element of mig matrix set to m_ij.)
		 -ma m_11 m_12 m_13 m_21 m_22 m_23 ...(Assign values to elements of migration matrix.)
		 -n i size_i   (popi has size set to size_i*N0 
		 -g i alpha_i  (If used must appear after -M option.)
	   The following options modify parameters at the time 't' specified as the first argument:
	 -eG t alpha  (Modify growth rate of all pop's.)
	 -eg t i alpha_i  (Modify growth rate of pop i.) 
	 -eM t mig_rate   (Modify the mig matrix so all elements are mig_rate/(npop-1)
	 -em t i j m_ij    (i,j-th element of mig matrix set to m_ij at time t )
	 -ema t npop  m_11 m_12 m_13 m_21 m_22 m_23 ...(Assign values to elements of migration matrix.)
	 -eN t size  (Modify pop sizes. New sizes = size*N0 ) 
	 -en t i size_i  (Modify pop size of pop i.  New size of popi = size_i*N0 .)
	 -es t i proportion  (Split: pop i -> pop-i + pop-npop, npop increases by 1.
		 proportion is probability that each lineage stays in pop-i. (p, 1-p are admixt. proport.
		 Size of pop npop is set to N0 and alpha = 0.0 , size and alpha of pop i are unchanged.
	 -ej t i j   ( Join lineages in pop i and pop j into pop j
		  size, alpha and M are unchanged.
	 -eA t popi num ( num Ancient samples from popi at time t
	  -f filename     ( Read command line arguments from file filename.)
	  -p n ( Specifies the precision of the position output.  n is the number of digits after the decimal.)
	  -a (Print out allele ages.)
 See msdoc.pdf for explanation of these parameters.

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Installation

Source code is obtained from https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13 and compiled using rand1.c

System

64-bit Linux