forkmanager takes too long when I set children

[Jaap van der Heijden]

Hi all,

I've made the script below to calculate the coverage per position of small pieces of strings. It works fine but when I tried to speed thing up for large files using forkmanager the script takes an awful lot of time when I set 2 parallel forks. Setting it to 0 works fine. Does anybody have an idea what is going wrong?

Kind Regards
Jaap

#!/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="theoretical 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;

[numberwhun]

I would help you if I had experience with forkmanager, but I have not used it. Hopefully someone will be able to help you.