Submitting awk script into cluster short.q

Thread Tools Search this Thread
# 1  
Submitting awk script into cluster short.q


I want to submit my awk script into cluster queue as my job takes about forty minutes to finish so I can not run it on the main node.
My awk script is like the following and I have three files. so, I write :

qsub -q short.q Myscript.awk file1 file2 file3

It submits the work into cluster but it gives an error after some seconds.
  if((2*nind+4) != NF){........}
   if(ID_num[i] in POP){
 if(nsnp%1000==0){print nsnp"\n"}

Thank you very much for yout help

Last edited by Neo; 11-06-2012 at 01:05 PM..
# 2  
What errors you are getting.?


why ORS=""..?



Previous Thread | Next Thread
Thread Tools Search this Thread
Search this Thread:
Advanced Search

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Simplifying awk/sed short pipeline

I have a file like this: FileName,Well,Sample Description,Size ,Calibrated Conc. ,Assigned Conc. ,Peak Molarity ,Area,% Integrated Area,Peak Comment,Observations 2017-11-15 - 13.49.50.D1000,EL1,Electronic Ladder,25,5.22,,321,0.803,,,Lower Marker 2017-11-15 - 13.49.50.D1000,EL1,Electronic... (6 Replies)
Discussion started by: Xterra
6 Replies

2. UNIX for Dummies Questions & Answers

Submitting cron job through script

I would like to run a script, as root, which will eventually set up cron job for a non privilege user. Please advice. (9 Replies)
Discussion started by: atanubanerji
9 Replies

3. OS X (Apple)

Shell Script to change desktop short cut Icon

I have installed my flash application using shell script. I have created short cut to desktop. Now i want to change the default short cut Icon. Please tell me script to change the short cut icon. ---------- Post updated at 12:54 AM ---------- Previous update was at 12:33 AM ---------- Working... (0 Replies)
Discussion started by: rohaneee
0 Replies

4. Shell Programming and Scripting

Help submitting jobs to cluster

Hi I am new to submitting jobs. I am trying to submit my perl file to the cluster. This is what my shell file looks like ( #!/bin/sh #$ -S /bin/sh cd data/projects/mydir/abbc perl followed by qsub It takes the qsub, but does nothing. I check... (1 Reply)
Discussion started by: theawknewbie
1 Replies

5. Shell Programming and Scripting

How do I do a short delay (milliseconds) in a shell script?

I need to put a small delay into a shell script. I'm looking for something smaller than "sleep" - a second is way too long. I want to sleep something like 10 milliseconds. I've tried "usleep" and "nanosleep", but the script doesn't recognize them. I'm using the bash shell but I'm willing to... (9 Replies)
Discussion started by: harmlesscat
9 Replies

6. Shell Programming and Scripting

translate a short csh script to bash

Hi, I have a csh: set NODES = `cat $HOST_FILE` set NODELIST = $TMPDIR/namd2.nodelist echo group main >! $NODELIST foreach node ( $NODES ) echo host $node >> $NODELIST end @ NUMPROCS = 2 * $#NODES I am very frustrated to translate it to bash: NODES = `cat... (3 Replies)
Discussion started by: rockytodd
3 Replies

7. UNIX Desktop Questions & Answers

Script that will display a short message

Can anyone point me to the right direction on how to write a simple script that will display a message on any terminal when implemented? Basically I need it so the script runs at a certain time, say April 30, 2010 and that the message will be displayed to me no matter which terminal I am logged... (2 Replies)
Discussion started by: jmack123
2 Replies

8. Shell Programming and Scripting

Looking for optimization advice on a short script

I already have a solution to my problem, but I'm looking to see if it can be made more succinct and faster. The problem: given a list, as shown below, extract the pathname for any file in a directory named 'ample' and return it's index into the list. The index is also in the data itself. Note that... (1 Reply)
Discussion started by: prigo
1 Replies

9. HP-UX

Sendmail not submitting Email on '.'

I have several HP/UX nodes running Sendmail 8.13 ...some work fine, some don't. When an Email is coming in, the 'DATA' command never ends. The other side of the connection gets to the point where it enters the '.' on a line by itself, but sendmail doesn't accept it...if fact it keeps on holding... (8 Replies)
Discussion started by: john_exonets
8 Replies

10. Shell Programming and Scripting

short script help

how do i find out the date of the last time the system was last booted from? (8 Replies)
Discussion started by: jodders
8 Replies

Featured Tech Videos