CD-HIT-PARA.PL(1)						   User Commands						 CD-HIT-PARA.PL(1)

NAME

       cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs

SYNOPSIS

       cd-hit-para.pl options

DESCRIPTION

	      This  script  divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel.  After
	      all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est.

	      You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option).

   Requirements:
	      1 When run this script over a network, the directory where you

	      run the scripts and the input files must be available on all the remote hosts with identical path.

	      2 If you choose "ssh" to submit jobs, you have to have

	      passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.

	      3 I suggest to use queuing system instead of ssh,

	      I currently support PBS and SGE

	      4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d

	      cd-hit-div cd-hit-div.pl must be in same directory where this script is in.

       Options

       -i input filename in fasta format, required

       -o output filename, required

       --P program, "cd-hit" or "cd-hit-est", default "cd-hit"

       --B filename of list of hosts,

	      requred unless -Q or -L option is supplied

       --L number of cpus on local computer, default 0

	      when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you
	      just use "--L 1" unless you have enough RAM for each cpu

       --S Number of segments to split input DB into, default 64

       --Q number of jobs to submit to queue queuing system, default 0

	      by default, the program use ssh mode to submit remote jobs

       --T type of queuing system, "PBS", "SGE" are supported, default PBS

       --R restart file, used after a crash of run

       -h print this help

       More cd-hit/cd-hit-est options can be speicified in command line

	      Questions, bugs, contact Weizhong Li at liwz@sdsc.edu

cd-hit-para.pl 4.6-2012-04-25					    April 2012							 CD-HIT-PARA.PL(1)