I have the next code that extract the sequences from a FASTQ file and convert in FASTA file; and the end make a count of the sequences available in the fasta file; the problem is the count is not Correct, the result is always less than the sequences available in the fasta output file.

FIRST SCRIPT

#!/usr/bin/perl -w
use strict;
use Getopt::Long;
use Term::ANSIColor;

# Variables
#--------------------------------------------------------------------------------------------------------------------------
my ($imput, $output, $line, $usage, $help_desciption, $help, $options, $op_desciption);


GetOptions (
            'i=s' => \$imput,
            'o=s' => \$output,
            'h'   => \$help,
            'op'  => \$options
            );


# help
#--------------------------------------------------------------------------------------------------------------------------
$help_desciption = (qq(
                    This Script extract the sequences from a FASTQ file and convert it to FASTA format
                    The sequences must be in the same file. It will generate a fasta file with the sequences
                    in the same order and name that are available in the imput file.

                    Example:
                    fastxQA -i file.fastq -o file.fasta
                        or  for more options see
                    fastxQA -op
                    ));

if ($help) {
    print "$help_desciption\n\n";
    exit;
}

# options
#--------------------------------------------------------------------------------------------------------------------------
$op_desciption = (qq(
           -i  = input  file in a .fastq format                     required
           -o  = output file in a .fa, .fas, .fasta or .txt format  required
           -h  = help                                               optional
           -op = options                                            optional
           ));


if ($options) {
    print "$op_desciption\n\n";
    exit;
}

# Error
#--------------------------------------------------------------------------------------------------------------------------

$usage = (qq(
          Error:
             Wrong Arguments

             Usage:
             fastxQA -i infile.fastq -o utfile.fasta

));

if (!$imput or !$output) {
    print color("red"), "$usage", color("reset"),"\n\n";
    exit;
}

# Open Data
#--------------------------------------------------------------------------------------------------------------------------
open FASTQIN, '<', "$imput" or die (color("red"), "\n\t\tCan't open $imput file\n\t\t\t or\n\t\t Does not exist such file", color("reset"),"\n\n");
open FASTAOUT, '>', "$output" or die (color("red"), "Can't genenate $output file", color("reset"),"\n\n");

# Processing Message
#--------------------------------------------------------------------------------------------------------------------------
print "\n";
$| = 1;
print colored("\t\t  This Process Will Take a While  ", "blue blink");
#sleep 2;
print "\r";


# Extract sequences
#--------------------------------------------------------------------------------------------------------------------------
while(
defined(my $head = <FASTQIN>) &&
defined(my $seq = <FASTQIN>) &&
defined(my $qhead = <FASTQIN>) &&    # te
defined(my $quality = <FASTQIN>)     # cuarta linea
){
  substr($head, 0, 1, '>'); #0 elimina el primer caracter (@) de la primer linea; el 1 remplaza la cantidad de caracteres, este caso solo 1 caracter


  print FASTAOUT $head, $seq;

}

# Count sequences "HAY UN ERROR DA 10 SEQUENCIAS MENOS "
#--------------------------------------------------------------------------------------------------------------------------
open COUNTERSEQ, '<', "$output" or die (color("red"), "Can't open $output file", color("reset"),"\n\n");
my $count = 0;

while( <COUNTERSEQ> ){
    chomp $_;
       if($_=~ /^>/g ) 
       {
             $count++; 
    }
}

# Close and Exit
#--------------------------------------------------------------------------------------------------------------------------
  close FASTQIN;
  close FASTAOUT;
  close COUNTERSEQ;
  print color("blue"),"                                      DONE                               \n\n", color("reset");
  print color("blue"),"              -  $count  sequences were converted to   $output File- \n\n", color("reset");
  exit;
  #--------------------------------------------------------------------------------------------------------------------------------------

However when I try the code for counting separately it works well:

SECOND SCRIPT

#!/usr/bin/perl -w
use strict;

my $infile =$ARGV[0];
open COUNTERSEQ, '<', $infile, or die;

my $count = 0;

while( <COUNTERSEQ> ){
    chomp $_;
       if($_=~ /^>/g )
       {
             $count++;
    }
}

print "$count\n";

Does anybody can help me to say what is the error in the connection in the first Script among the extracting section and the count section!?

Thanks so much!