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my $count = $result_buffer->{$id}->{$pwm};

 my $count = count_pwm_num($pwm,$seq_1,$seq_2);

if($count != 0) {
     $output_temp_handle->print($id);
...
     $output_temp_handle->print($id);
     $output_temp_handle->print("\t$pwm\t0\n");
}

$pm->start and next PWM;