I am programming perl for a while now but mysql, and the combination of perl with mysql is very new to me. I wrote a perl script that is supposed to do kmedoids-clustering of several thousand promoters (human genome).

Many instances of this script are running on a Grid Engine cluster. When I run this script with a random selection of a few hundred promoters only, everything works fine.

But now I tried to cluster the full dataset of several thousand promoters and get this error:

"DBD::mysql::st fetchrow_array failed: fetch() without execute() at chipchip.pl line 144, <L3> line 14446. "

Here is the part of my script where it happens, I think:

foreach $item (@{$clusters}) {
    $ID = $units[$i][0];

    $query = "select * from finalLevel3 where id=\"$ID\";";
    $sth = $dbh -> prepare($query);
    $sth -> execute;
    @row = $sth -> fetchrow_array;

    # convert the mysql result back to a string again
    $promoter_line = join "\t", @row;
    $promoter_line .= "\n";
    
    $parser_hash{$item} .= $promoter_line;
    $i++;
}

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I found a thread in this forum which I think is a very similar problem and the solution, however I must say that I simply don't understand how to solve this and what's going on. That thread is node 729564. I'm happy that this problem seems already to be solved but I simply don't understand the solution - a more verbose explanation would be very, very much appreciated.

Do I need two separate $dbh - handles? If yes do I need to connect them separatedly?

I would be very thankful if someone could explain to me how to fix this. Also, the thing is that this error only shows up if I do the clustering on the whole dataset (2 days runtime on Grid Engine), so it would be superduper cool if I could get it right the first or second time because it takes so long to reproduce the error. Thank you.

In reply to perl, mysql: "fetchrow_array failed: fetch() without execute()" by gojira

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