system function only returns the exit status of the command; if you want to capture the output, you should use backticks:

$result = `command`;
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Then, you can write this output to wherever you want it with something like this:

open OUTFILE, "> /path/to/outfile.txt";
print OUTFILE $result;
close OUTFILE;
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Alternately, if you do not want to process the output in Perl, you can just do something like this:

system("command > /path/to/result.txt");
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However, in this case you probably wouldn't need to use Perl for it at all...

HTH