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cd-hit-2d-para - Online in the Cloud

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


cd-hit-2d-para.pl 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

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 cd-hit-div.pl must be

in same directory where this script is in.


-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 [email protected]

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