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Top Forums UNIX for Dummies Questions & Answers Submitting awk script into cluster short.q Post 302727543 by Homa on Tuesday 6th of November 2012 11:39:33 AM
Old 11-06-2012
Submitting awk script into cluster short.q

Hello,

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.
Code:
BEGIN{
OFS=ORS=""
}
{
..........
  nsnp++
  if((2*nind+4) != NF){........}
  for(i=1;i<=nind;i++){
   if(ID_num[i] in POP){
      pos_deb=2*(i-1)+5
     {...........}
      }
 }
 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..
 

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DIFF3(1)						      General Commands Manual							  DIFF3(1)

NAME
diff3 - 3-way differential file comparison SYNOPSIS
diff3 [ -ex3 ] file1 file2 file3 DESCRIPTION
Diff3 compares three versions of a file, and publishes disagreeing ranges of text flagged with these codes: ==== all three files differ ====1 file1 is different ====2 file2 is different ====3 file3 is different The type of change suffered in converting a given range of a given file to some other is indicated in one of these ways: f : n1 a Text is to be appended after line number n1 in file f, where f = 1, 2, or 3. f : n1 , n2 c Text is to be changed in the range line n1 to line n2. If n1 = n2, the range may be abbreviated to n1. The original contents of the range follows immediately after a c indication. When the contents of two files are identical, the contents of the lower-numbered file is suppressed. Under the -e option, diff3 publishes a script for the editor ed that will incorporate into file1 all changes between file2 and file3, i.e. the changes that normally would be flagged ==== and ====3. Option -x (-3) produces a script to incorporate only changes flagged ==== (====3). The following command will apply the resulting script to `file1'. (cat script; echo '1,$p') | ed - file1 FILES
/tmp/d3????? /usr/lib/diff3 SEE ALSO
diff(1) BUGS
Text lines that consist of a single `.' will defeat -e. Files longer than 64K bytes won't work. DIFF3(1)
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