[ensembl-dev] DBD failed to fetch homology data - server shutdown in progress

[Mark Brown]

We used to be able to run the following script without problem for previous
releases.
It appears a simple join among homolgy,homology_member, and member tables
times out.

Error message returned by executing the perl script below is:
DBD::mysql::st execute failed: Server shutdown in progress at ./t.pl line
10.
DBD::mysql::st fetchrow_array failed: fetch() without execute() at
./t.plline 12.

Maybe some data columns are not indexed appropriately, or table corrupted?
Thanks.

===========================
#!/usr/local/bin/perl -w
use DBI;
use Carp;
my $dbh=DBI->connect("dbi:mysql:ensembl_compara_63:
ensembldb.ensembl.org:5306", "anonymous", "");
$dbh->{RowCacheSize}=16*1024;
my $s_sql="SELECT m.taxon_id TAX_ID,h.homology_id HOMOLOGY_ID,m.stable_id
GENE_ID,h.description DESCRIPTION FROM homology h,homology_member hm,member
m WHERE h.homology_id=hm.homology_id AND hm.member_id=m.member_id AND
m.taxon_id=9606 AND m.source_name ='ENSEMBLGENE'";
  my $sth = $dbh->prepare($s_sql) or confess "Preparing: , ".$dbh->errstr;
  $sth->execute() or confess "Executing: ".$dbh->errstr;
  open(OUT, "> out.txt");
  while (my @data = $sth->fetchrow_array()) {
    print OUT join("\t", @data), "\n";
  }
  $dbh->disconnect;
  close(OUT);
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