my database [...]
This gives me a segmentation fault

Wow. Did you report that back to wherever that database was manufactured?

(For instance, if it were PostgreSQL they would want to know about such a awful bug.)

(And, by the way, if it were postgres you could use md5 as a db-function, no need for external checksumming.)

#!\C:\Strawberry\perl\bin\perl

use strict;
use warnings;
use DBI;
use DBD::mysql;
use String::CRC32;

#DATA SOURCE NAME
my $dsn = "dbi:mysql:database=$database;host=$host;port=$port";

#PERL DBI CONNECT
my $dbh=DBI->connect($dsn,$user,$pw, {
    PrintError  => 0,
    RaiseError  => 1,
    AutoCommit  => 1,    
}) or die  $DBI::errstr;

#Read input file to load into DB
open(INFILE, "<$ARGV[0]") or die "cannot open file:$!\n";


<INFILE>; #skip header
for(<INFILE>){
    #split line
    my @line=split("\t", $_);

    #check correct number of columns
    if (scalar(@line)>=11) {
        #parse columns
        my $chr=$line[0];
        my $pos=$line[1];
        my $sequence=$line[2];
        
        #insert sequence
        my $crc32=crc32("$sequence"); #check crc32 of sequence
        print unpack($crc32)."\n";
        my $th=$dbh->prepare(qq(SELECT COUNT(1) FROM Sequence WHERE Se
+q_Checksum=$crc32));
        $th->execute();
        my $test=$th->fetch()->[0];
        print "$test\n";

        #if ($th->fetch()->[0]) {
        #    print "Sequence already in database!\n";
        #}
        #else {
        #    print "New sequence detected, inserting into database wit
+h unique checksum.\n";
        #    $dbh->do("INSERT INTO Sequence(Sequence) VALUES($sequence
+)");
        #    $dbh->do("INSERT INTO Sequence(Seq_Checksum) VALUES($crc3
+2)");
        #    
        #}
        #     

        
    }
    
   
    
}
[download]

ah I see how to do placeholder. That's a neat trick.

my $th=$dbh->prepare(qq(SELECT COUNT(1) FROM Sequence WHERE Seq_Checks
+um=?));
$th->execute($crc32);
[download]