---
name: "cd-hit-2d-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-2d-para"
---

# cd-hit-2d-para(1)

divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs

## 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