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 or cd-hit-est.

  • 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 cd-hit-2d cd-hit-est cd-hit-est-2d

  • cd-hit-div 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