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