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origo-submit 0.1.1 (Default branch)
05-17-2008
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CD-HIT-PARA.PL(1) User Commands CD-HIT-PARA.PL(1) 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 liwz@sdsc.edu cd-hit-para.pl 4.6-2012-04-25 April 2012 CD-HIT-PARA.PL(1)