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cd-hit-para - Online in the Cloud

Run cd-hit-para in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command cd-hit-para that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs

SYNOPSIS


cd-hit-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 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).

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 [email protected]

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