Looks like you're opening a file named <pid>.out. This may work for you. ($$ is the current process id) 
for (my $i = 0 ; $i < @array1 ; $i++)
{
  open(OUT, ">$i.out") or die "can't open $i.out: $!\n";
  print OUT ">" . $array1[$i] . ">" . $array2[$i] . "\n\n\n";
  close OUT;
}

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In reply to Re: printing to new output files within a loop by amw1
in thread printing to new output files within a loop by Anonymous Monk

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