perl -c Brapa0101-db.pl
Brapa0101-db.pl syntax OK

DBD::mysql::st execute failed: called with 9 bind variables when 0  are needed at Brapa0101-db.pl.bk line 45, <FILE> line  41174.

#!/usr/bin/perl -w

use strict;
use DBI;

# # # # # # # # # # # # # # # #  # # # # # # # # # # # # # # 
#The database "Brapa0101_db" has been created with mysql
#mysql> CREATE database Brapa0101_db;
# # # # # # # # # # # # # # # #  # # # # # # # # # # # # # # 

my $DataBaseName="Brapa0101_db";
my $DataBaseHost="localhost";
my $MySQLUser="myql_account";
my $MySQLUserPass="passwrdxyzt";
my $dsn="DBI:mysql";
my $Table="table01" ;
    

my $dbh = DBI->connect("$dsn:$DataBaseName:$DataBaseHost", $MySQLUser, $MySQLUserPass) 
            or die "Cannot connect: " . $DBI::errstr;
   my $sql = qq/INSERT INTO $Table 
                      (run, geneid,            seqtype,     scaffold,  seqstart, seqend, seqstrand,  seqlength, cdsseq)
              VALUES( int, char(20) primary key, char(20), char(100), int,   int, char(10), int,    text(40000))
            /;
##############Example rows of the file /path/to/MySQL_Study/Brapa1.1-database/Brassica_rapa.20100830.cds.tab5"
#    Run    Gene    mRNA    Scaffold    Start    End    Strand    Length    Sequence
#    1    Bra000001    [mRNA]    locus=Scaffold000001    3252        5836        +    2584    ATGGGGAAGATCTTGAAAACTAAGTCTT
#    2    Bra000002    [mRNA]    locus=Scaffold000001    6640        9120        -    2480    ATGGAGGAAGTAAGGAAGATGGGTTGTAT
#    3    Bra000003    [mRNA]    locus=Scaffold000001    21211    22012    +    801    ATGAGCTCTGTTTGTGGTAAGCTGGATTT
#    4    Bra000004    [mRNA]    locus=Scaffold000001    25599    25973    +    374    ATGATTCGCCGTCTATTCTCGTCTCTGACT.
#    5    Bra000005    [mRNA]    locus=Scaffold000001    26822    28864    -    2042    ATGGCGGCAGCTAGACGATT..
#    6    Bra000006    [mRNA]    locus=Scaffold000001    29480    29791    -    311    ATGTC...............
my $sth = $dbh->prepare($sql);

my $file_name="/path/to/MySQL_Study/Brapa1.1-database/Brassica_rapa.20100830.cds.tab5";

open(FILE, "<$file_name") or die("Cannot open the file named $file_name to read!");
     
foreach my $line (<FILE>) {
    # next if $_=~ m/Run\t/;                #This $_ has caused many headaches on me, 
    
     next if $line=~ m/Run\t/;                #This is the right syntax 
     chomp $line;
  my @fields = split(/\t/, $line);
    $sth->execute(@fields);
}

while (my $row = $sql->fetchrow_arrayref) {
        print join("\t", @$row), "\n";
    }
$dbh->disconnect;