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