G'day plagent,

You haven't shown the code that actually generates the report. That makes it rather difficult to troubleshoot.

The actual output you show has staggered columns. This suggests to me that data for various columns is either whitespace or empty strings. The latter could be the result of an uninitialized value being treated as "". The warnings pragma will alert you to this.

Other potential issues include:

• $id is set on each iteration of the outer loop but never used.
• $count is set on each iteration of the inner loop but never used.
• You haven't shown any declaration for $count. The strict pragma will alert you to undeclared variables.
• You're calling count_pwm_num() in list context (($count) = ...) which seems inappropriate for a function which returns a number. Obviously, as you haven't shown the code for count_pwm_num(), that's just a guess on my part.

If one or more of those suggestions and guesses lead to a solution, that's great. If not, you'll need to post more code for us to help you further. Also include any output from the two pragmata I mentioned: given they're both lexically scoped, it's important to show where in your code that you've included them.

Thanks, Ken. I updated the source code, and hope this light version will explain my trouble. In fact, there was complaint from running the above code. It is "Use of uninitialized value $count". The code of this line is

my $count = $result_buffer->{$id}->{$pwm};
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The missing value here indicates that this piece of code

 my $count = count_pwm_num($pwm,$seq_1,$seq_2);
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did not perform its function when parameters were transferred here. $pwm is from list @ciona_pwm_array. Because after executing those lines, the result will catch either 1 or 0,

if($count != 0) {
     $output_temp_handle->print($id);
     $output_temp_handle->print("\t$pwm\t1\n");
}
else {
     $output_temp_handle->print($id);
     $output_temp_handle->print("\t$pwm\t0\n");
}
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However, as shown in result table, several values were missed from certain rows, (row c missed value 1 in column B, row b missed value 1 in column A. The missing values have no specific pattern, and it seems randomly lost. I doubted for some reason it did not execute this code

$pm->start and next PWM;
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But I do not know why. Thanks.

I wrote a mini code for this problem which replicates my puzzle.

#!/usr/bin/perl

use strict;
use Parallel::ForkManager;

my $pm = Parallel::ForkManager->new(10);

foreach my $j (1..100) {
    LINKS:
    for my $i (1..10) {
        $pm->start and next LINKS;
        my $num = count($i);
        print $num,"\t";
        $pm->finish;
    }
    print "\n";
    $pm->wait_all_children;
}

sub count {
    my $num = shift;
    return $num + 1;
}
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I expected each row should generate ten numbers from 2 to 11. However, several rows will miss values. Even worse, several rows output 11 numbers instead of 10 numbers, and have replicate, for example, 10 appear twice. Why?