#!/usr/bin/perl -w
[download]
use strict;
&sub1; #generates a text file (rep_set.txt)
system('python //macqiime/QIIME/bin/assign_taxonomy.py -i rep_set.txt 
+-o .'); #generates second txt file

if ( $? == -1 )
{
  print "command failed: $!\n";
}
else
{
  printf "command exited with value %d", $? >> 8;
}


&sub2; #reads the second text file

[download]

Try your script this way of checking the exit status of your python script.

All is well

In reply to Re^4: system() issue by vinoth.ree
in thread system() issue by Anonymous Monk

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