#!/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.