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#your code
#my $infile = $ARGV[0];  
...
#corrected code
my $infile = $ARGV[0];
my $infile2 = $ARGV[1];

#yourcode
while (<INFILE>){
    chomp;
...
        next;
    }
}

while (<INFILE>){
    chomp;
...
        }
    }
}}