CD-HIT-2D-PARA.PL

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