SYNOPSIS options


  • 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).


  • 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 must be

  • in same directory where this script is in.



input filename for 1st db in fasta format, required -i2 input filename for 2nd db in fasta format, required


output filename, required


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


filename of list of hosts, requred unless -Q or -L option is supplied


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


Number of segments to split 1st db into, default 2 --S2 Number of segments to split 2nd db into, default 8


number of jobs to submit to queue queuing system, default 0 by default, the program use ssh mode to submit remote jobs


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


restart file, used after a crash of run


print this help

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