my $cmd1 = "java -Xmx2G -jar $rootdir/celConverter/CelFileConverter.jar -m $rootdir/celConverter/Snp6FeatureMappings.csv -c $rootdir/cdf/GenomeWideSNP_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_Runtime/v710/ $file $rootdir/info/ $rootdir/outdir/raw/ $rootdir/outdir/output/  $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;
  }
}