.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH CD-HIT-PARA.PL "1" "September 2018" "cd-hit-para.pl 4.6.8" "User Commands"
.SH NAME
cd-hit-para.pl \- divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs
.SH SYNOPSIS
.B cd-hit-para.pl
\fI\,options\/\fR
.SH DESCRIPTION
.IP
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.
.IP
You can also use it to divide big jobs on a single computer if
your computer does not have enough RAM (with \fB\-L\fR option).
.SS "Requirements:"
.IP
1 When run this script over a network, the directory where you
.IP
run the scripts and the input files must be available on
all the remote hosts with identical path.
.IP
2 If you choose "ssh" to submit jobs, you have to have
.IP
passwordless ssh to any remote host, see ssh manual to
know how to set up passwordless ssh.
.IP
3 I suggest to use queuing system instead of ssh,
.IP
I currently support PBS and SGE
.IP
4 cd\-hit cd\-hit\-2d cd\-hit\-est cd\-hit\-est\-2d
.IP
cd\-hit\-div cd\-hit\-div.pl must be in same directory where
this script is in.
.PP
Options
.HP
\fB\-i\fR input filename in fasta format, required
.HP
\fB\-o\fR output filename, required
.HP
\fB\-\-P\fR program, "cd\-hit" or "cd\-hit\-est", default "cd\-hit"
.HP
\fB\-\-B\fR filename of list of hosts,
.IP
requred unless \fB\-Q\fR or \fB\-L\fR option is supplied
.HP
\fB\-\-L\fR number of cpus on local computer, default 0
.IP
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
.HP
\fB\-\-S\fR Number of segments to split input DB into, default 64
.HP
\fB\-\-Q\fR number of jobs to submit to queue queuing system, default 0
.IP
by default, the program use ssh mode to submit remote jobs
.HP
\fB\-\-T\fR type of queuing system, "PBS", "SGE" are supported, default PBS
.HP
\fB\-\-R\fR restart file, used after a crash of run
.HP
\fB\-h\fR print this help
.PP
More cd\-hit/cd\-hit\-est options can be speicified in command line
.IP
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu