Hi All, I've got this piece of code below to calculate the coverage of small pieces of strings across the genome (large string). The script works fine when I set 0 children. Setting children to 1 or 2 doesn't work (takes really long). Does anybody have an idea what is going wrong? 
#!/usr/local/bin/perl -w
use Parallel::ForkManager;
use strict;

if(scalar(@ARGV) != 3){
    print "Please use the correct parameters\nUsage: bowtie2wiggle.pl 
+-infile -outfile- -processes-\n";
    exit();
}

my $pm = new Parallel::ForkManager($ARGV[2]); 
my %hash=();
open (IN, $ARGV[0]);
while (<IN>){
    $pm->start and next;
    $_ =~ s/\n|\r//;
    my @element=split(/\t/,$_);
    $element[2] =~ s/T//;
    for (my $i=1;$i<=length($element[4]);$i++){
        $hash{$element[2]}{($element[3]+$i)}{coverage}++;
    }
    $pm->finish;
}
$pm->wait_all_children;
close IN;

open (OUT, ">$ARGV[1]");
print OUT 'track type=wiggle_0 name="'.$ARGV[0].'" description="theore
+tical coverage from '.$ARGV[0].'" visibility=full autoScale=on color=
+50,150,255'."\n";

my $old="";
foreach my $chromosome (sort keys %hash){
    print OUT "variableStep chrom=chr$chromosome span=1\n";
    foreach my $position (sort {$a<=>$b} keys %{$hash{$chromosome}}){
        if ($old ne "" && $old != ($position-1)){
            print OUT "variableStep chrom=chr$chromosome span=1\n";
        }
        print OUT "$position $hash{$chromosome}{$position}{coverage}\n
+";
        $old=$position;
    }
}
close OUT;


#######Input data:
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr18    20832586    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    1    20:T>C,22:C>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr3    159753225    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    0    26:G>A,36:T>C
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr2    26523236    GCAGATCA
+CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA  
+  T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`d
+dddd^dda    0    26:G>A,53:A>G
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr6    122836749    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    0    26:G>A,49:C>G
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr3    12482979    GCAGATCA
+CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA  
+  T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`d
+dddd^dda    3    22:C>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr16    85386061    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    3    22:C>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr8    74059852    GCAGATCA
+CCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA  
+  T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`d
+dddd^dda    3    22:C>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr13    34357600    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    3    22:C>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chr12    31386168    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    1    22:C>A,72:G>A
HWI-EAS384:7:1:1124:2949#TCTANN/1    -    chrX    134915278    GCAGATC
+ACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGCAAAAACCTGTCTCTACTAAAAATACAA 
+   T^TY^Y]\\^adT_a^^^\Ta__aa`][^YT^T\aTT`]KY_^_YY`^[T_b]bYeeff\ffbff`
+ddddd^dda    1    22:C>A,72:G>A

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In reply to parallel::forkmanager takes too long setting children by Jaap1

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