---
name: "cd-hit-para"
section: "1"
platform: "linux"
package: "cd-hit"
version: "4.8.1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cd-hit-para"
---

# cd-hit-para(1)

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

## 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

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  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.

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  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:

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  1 When run this script over a network, the directory where you

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  run the scripts and the input files must be available on all the remote hosts with identical path.

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  2 If you choose "ssh" to submit jobs, you have to have

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  passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.

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  3 I suggest to use queuing system instead of ssh,

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  I currently support PBS and SGE

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  4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d

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  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,

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  requred unless **-Q** or **-L** option is supplied

**--L** number of cpus on local computer, default 0

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  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

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  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

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  Questions, bugs, contact Weizhong Li at liwz@sdsc.edu