hello all
im trying to use in sun Solaris the information received from the top command
now i several machines that dont have install the top program so when im running the script im geting error
saying after im running this code :
set MemoryInfo = `top | grep Memory`
if (... (2 Replies)
i installed x windows redhat linux 9.0 in my pc.
but the problem is when i run cc command for c programme .....bash:cc: command not found printed ...........i set the path for bash ............with the help of PATH=$PATH....................still it is not working .........please guide me. (4 Replies)
Hi guys,
I do apologise if this question has been asked before. I am currently running Solaris 10 on a x86 architecture. Now, the problem I am having relates to the issuing of commands, for example if I am trying to find out the ipaddress of the machine I would issue the command 'ipconfig -a |... (2 Replies)
I'm using Terminal in MAC OS X, and new to this.
I don't know what happened to the path. I always get "command not found".
For example, this is some of what I get:
-bash: ls: command not found
-bash: touch: command not found
What should I do to return the terminal to normal?
... (0 Replies)
I have installed Solaris recently. I was doing "for file in *.c; ...." at the command prompt, it says for: command not found. I tried changing shells, but still wouldn't work.
Any ideas? (7 Replies)
I created a script that I need to run from time to time, but get this error message. To get it working again I run this command from time to time:
export PATH="$PATH:~/scripts"
I put all my automated scripts in the /scripts directory and would like to run my scripts from any directory... (5 Replies)
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
Trying to run script but everytime I do I get teh following error message
line 4:
I have attempted... (5 Replies)
I am running the export command within a view to use that value inside my build script. But while executing it it is saying "export command not found"
My code is as follows:
--------------------------
#!/bin/sh
user="test"
DIR="/bldtmp/"$user
VIEW="test.view1"
echo "TMPDIR before export... (4 Replies)
Hi Experts,
I am very much new to linux scripting, I am currently working on reducing my manual work and hence writing a script to automate few task.
I am running below command to snmpwalk the router..
snmpwalk -v 3 -u WANDL_SU -a MD5 -A vfipmpls -x DES -X VfIpMpLs -l authPriv... (19 Replies)
Hi all,
ar command not found on Solaris 10 version.
We can execute under ./ar command /usr/ccs/bin directory.
However, we want to execute ar command anywhere.
We add to /usr/ccs/bin entry under /etc/profile file shown as below.
umask 002
trap 2 3
... (2 Replies)
Discussion started by: ziosnim
2 Replies
LEARN ABOUT DEBIAN
cdhit-est
CD-HIT-EST(1) User Commands CD-HIT-EST(1)NAME
cdhit-est - run CD-HIT algorithm on RNA/DNA sequences
SYNOPSIS
cdhit-est [Options]
DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ======
Options
-i input filename in fasta format, required
-o output filename, required
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical
amino acids in alignment divided by the full length of the shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino
acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see
options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-M memory limit (in MB) for the program, default 800; 0 for unlimitted;
-T number of threads, default 1; with 0, all CPUs will be used
-n word_length, default 10, see user's guide for choosing it
-l length of throw_away_sequences, default 10
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of
the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the
representative of the cluster can not be bigger than 60
-aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing
gaps) must not be more than 10% of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail-
ing gaps) must not be more than 10% of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more
than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use
-B 1 for huge databases
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus-
ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but
either 1 or 0 won't change the representatives of final clusters
-r 1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+ strand alignment
-mask masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
-match matching score, default 2 (1 for T-U and N-N)
-mismatch
mismatching score, default -2
-gap gap opening score, default -6
-gap-ext
gap extension score, default -1
-bak write backup cluster file (1 or 0, default 0)
-h print this help
Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu For updated versions and information, please
visit: http://cd-hit.org
cd-hit web server is also available from http://cd-hit.org
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
Godzik. Bioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659
cd-hit-est 4.6-2012-04-25 April 2012 CD-HIT-EST(1)