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cd-hit-2d-para

CD-HIT-2D-PARA.PL(1)						   User Commands					      CD-HIT-2D-PARA.PL(1)

NAME

       cd-hit-2d-para.pl - divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs

SYNOPSIS

       cd-hit-2d-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-2d or cd-hit-est-2d.

	      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-2d 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 for 1st db in fasta format, required

       -i2 input filename for 2nd db in fasta format, required

       -o     output filename, required

       --P    program, "cd-hit-2d" or "cd-hit-est-2d", default "cd-hit-2d"

       --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 1st db into, default 2

       --S2 Number of segments to split 2nd db into, default 8

       --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-2d/cd-hit-est-2d options can be speicified in command line

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

cd-hit-2d-para.pl 4.6-2012-04-25				    April 2012						      CD-HIT-2D-PARA.PL(1)

UNIX for Dummies Questions & Answers