02-19-2004
Hi Perderabo / Oombera,
Thanks for your help and very detailed explanation !!
There was one thing that hit my attention :
quote:
--------------------------------------------------------------------------------
In the 60's I used to type in fortran programs
--------------------------------------------------------------------------------
I don't think I was there yet by that time and You just showed your self a little
Thanks a lot for your explenation !! I can rest now in the knowledge of knowing there is no solution possible for me
Best regs David
(sorry i hit edit on mistake) - optimus_p
Last edited by Optimus_P; 02-19-2004 at 10:33 AM..
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LEARN ABOUT DEBIAN
cd-hit-2d-para
CD-HIT-2D-PARA.PL(1) User Commands CD-HIT-2D-PARA.PL(1)
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
cd-hit-2d-para.pl 4.6-2012-04-25 April 2012 CD-HIT-2D-PARA.PL(1)