First, your inner loop reads the ODIR directory all the way through, so there's nothing to read in the second iteration of the outer loop. Second, since you've opened the directory and are putting files in it while you have it open, I don't know that there's any guarantee that you won't miss a file. You could fix both problems by opening ODIR just before the start of the second loop. Alternatively, you could use a glob to find the matching filenames, rather than scanning through all of them.

However, there's a better way: Since you already know the name of the file, there's no reason to scan through the directory for it. Instead, just open your file. Since you pass in $sample on the command line, there's no reason to use the opendir / readdir and regular expression.

my $cmd1 = "java -Xmx2G -jar $rootdir/celConverter/CelFileConverter.ja
+r -m $rootdir/celConverter/Snp6FeatureMappings.csv -c $rootdir/cdf/Ge
+nomeWideSNP_6.fromDB.cdf -s $celdir/ -t $rootdir/outdir/raw";
system($cmd1);

my $dir = "$rootdir/outdir/output2/$sample" . "_feature.TXT";

opendir(DIR, "$rootdir/outdir/raw") || "Cannot open the directory $!\n
+";

foreach my $file (readdir(DIR)){
  if($file =~ /feature_intensity$/){
 
    #my $cmd = "sh run_preprocessing.sh $rootdir/Matlab_Compilet_Runti
+me/v710/ $file $rootdir/info/ $rootdir/outdir/raw/ $rootdir/outdir/ou
+tput/  $rootdir/outdir/ PRIMARY 0.5";
    #warn "Running $cmd... \n"; 
    #system($cmd); #outputs ploidy_3456_feature.TXT.csv
  
    #output from the previous system cmd. 
    $file2 = "ploidy_" . $sample . "_feature.TXT.csv";
    open FILE, "<", $dir/$file2"
        or "Cannot open the file $file2 $!\n"; 
    while(<FILE>){
      chomp;
      my ($in_pi,$in_ploidy,$in_alpha) = split(/,/);
      my $cmd2 = "sh run_HMM.sh $rootdir/Matlab_Compilet_Runtime/v710/
+ $file $rootdir/info/ $rootdir/outdir/output/ $rootdir/outdir/ 10 $in
+_pi $in_ploidy $in_alpha";
      warn "Running $cmd2\n";
      system($cmd2);
    }
    close FILE;
  }
}
[download]

I've cleaned up your indentation a little to make the code easier to follow, and used the three-argument form of open, as a reminder that it's generally accepted as the better form to use.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

Hi Thanks!That make sense now and has solved the issue :) Thanks a lot once again

Unless you actually use a key based lookup elsewhere in the code you may be better to use nested arrays rather than nested hashes. Consider:

#!c:\Perl\bin\perl
use warnings;
use strict;

use constant KANRI_01_0 => 0x00000001;    # TBC
use constant KANRI_01_1 => 0x00000002;    # TBC
use constant KANRI_02_0 => 0x00000004;    # TBC
use constant KANRI_02_1 => 0x00000008;    # TBC
use constant KANRI_03_0 => 0x00000010;    # TBC
use constant KANRI_04_1 => 0x00000020;    # TBC
use constant KANRI_04_2 => 0x00000040;    # TBC
use constant KANRI_04_3 => 0x00000080;    # TBC
use constant KANRI_04_4 => 0x00000100;    # TBC
use constant KANRI_05_1 => 0x00000200;    # TBC
use constant KANRI_05_2 => 0x00000400;    # TBC
use constant KANRI_06_1 => 0x00000800;    # TBC
use constant KANRI_07_1 => 0x00001000;    # TBC
use constant KANRI_07_2 => 0x00002000;    # TBC
use constant KANRI_07_3 => 0x00004000;    # TBC
use constant KANRI_07_4 => 0x00008000;    # TBC
use constant KANRI_07_5 => 0x00010000;    # TBC
use constant KANRI_08_1 => 0x00020000;    # TBC

my @menu = (
    [Outer1 => [
        [O1Inne1 => KANRI_04_1],
        [O1Inne2 => KANRI_04_2],
        [O1Inne3 => KANRI_04_3],
        [O1Inne4 => KANRI_04_4],
    ]],
    [Outer2 => [[O2Inne1 => KANRI_05_1]]],
    [Outer3 => [[O3Inne1 => KANRI_06_1]]],
    [Outer4 => [
        [O4Inne1 => KANRI_07_1],
        [O4Inne2 => KANRI_07_2],
        [O4Inne3 => KANRI_07_3],
        [O4Inne4 => KANRI_07_4],
        [O4Inne5 => KANRI_07_5],
    ]],
    [Outer5 => [[O5Inne1 => KANRI_08_1]]],
);


for my $mainMenuItem (@menu) {
    print "$mainMenuItem->[0]\n";
    for my $subMenuItem (@{$mainMenuItem->[1]}) {
        print "$subMenuItem->[0] = $subMenuItem->[1]   ";
    }
    print "\n";
}
[download]

Prints:

Outer1
O1Inne1 = 32   O1Inne2 = 64   O1Inne3 = 128   O1Inne4 = 256   
Outer2
O2Inne1 = 512   
Outer3
O3Inne1 = 2048   
Outer4
O4Inne1 = 4096   O4Inne2 = 8192   O4Inne3 = 16384   O4Inne4 = 32768   
+O4Inne5 = 65536   
Outer5
O5Inne1 = 131072
[download]