See the response from vinoth.ree. system() has a return value. A return value of 0 is good. Other return values indicate various types of problems. One thing you can do is print the value returned by system.

my $rc = system( 'python //macqiime/QIIME/bin/assign_taxonomy.py -i re
+p_set.txt -o .');
print "system returned $rc, \$? is $?\n";
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see the perdoc on system in perlfunc for more details