[ensembl-dev] slow response and problems to receive mouse ancestral sequence. API 83

Christian Groß - EWI C.Gross at tudelft.nl
Mon Mar 7 11:01:58 GMT 2016

Dear Ensembl Developer Team,

My name is Christian Groß  and I am a PhD student at the TUDelft in the Netherlands. For a week I try to download the ancestral sequence of the Mouse-Rat ancestor. To do that I use the "get_ancestral_sequence.pl" which is provided by the PERL ensemble-API. I modified that script a slightly bit to make it work for my purposes.
I changed this
(140): my $species_name = "Homo sapiens";
(141): my $alignment_set = "primates";
my $species_name = "Mus musculus";
my $alignment_set = "mammals";
and I replaced this
(161): if ($registry_file) {
(162):   die "Registry file '$registry_file' doesn't exist\n" if (!-e $registry_file);
(163):   $reg->load_all($registry_file, 1);
(164): } elsif ($url) {
(165):   $reg->load_registry_from_url($url, 1);
(166): } else {
(167):   $reg->load_all();
(168): }
by this.
# Auto-configure the registry
        -host=>"ensembldb.ensembl.org", -user=>"anonymous",

I started the modified script on one of our servers but it runs incredible slowly, most of the time it is in a sleeping state and waits for a response from the ensembl servers. The first try was killed by our server because it extended a 1 ½ day limit. Therefore I started it again on a different server but the connection to the ensemble MySQL was lost after  2 days and 4hours. Within these two days only  1017MB of the ancestral sequence were downloaded.
Is there any way to speed up the download or to start the download at the point at which it stopped? Has my request a low priority because I use the auto-configure registry?
I would be really glad if you could help me in this case or point me to a different method to extract the ancestral sequence from the server.
Down below you will find the entire output message from starting that script until the thrown exception.
Much thanks in advance.

Christian Groß

(dato-env2)gross016 at assembly:/mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/scripts/ancestral_sequences$ perl get_ancestral_sequence_mouse.pl
UNIVERSAL->import is deprecated and will be removed in a future perl at /mnt/scratch/gross016/bin/nobackup/ensemble_api/BioPerl-1.6.1/Bio/Tree/TreeFunctionsI.pm line 94.
Found MLSS mlss_id=780 name='17 eutherian mammals EPO'
DBD::mysql::st execute failed: Lost connection to MySQL server during query at /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 170.

-------------------- EXCEPTION --------------------
MSG: Detected an error whilst executing SQL 'SELECT gat.node_id, gat.parent_id, gat.root_id, gat.left_index, gat.right_index, gat.distance_to_parent, gat.left_node_id, gat.right_node_id, ga.genomic_align_id, ga.genomic_align_block_id, ga.method_link_species_set_id, ga.dnafrag_id, ga.dnafrag_start, ga.dnafrag_end, ga.dnafrag_strand, ga.cigar_line, ga.visible FROM ( (genomic_align_tree gat)  LEFT JOIN genomic_align ga ON gat.node_id = ga.node_id) WHERE gat.node_id = ?  LIMIT 1': DBD::mysql::st execute failed: Lost connection to MySQL server during query at /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 170.

STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:171
STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch_one /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:270
STACK Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_node_by_node_id /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/NestedSetAdaptor.pm:98
STACK Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor::fetch_parent_for_node /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/NestedSetAdaptor.pm:118
STACK Bio::EnsEMBL::Compara::NestedSet::parent /mnt/scratch/gross016/bin/nobackup/ensemble_api/ensembl-compara/modules/Bio/EnsEMBL/Compara/NestedSet.pm:277
STACK main::dump_ancestral_sequence get_ancestral_sequence_mouse.pl:290
STACK toplevel get_ancestral_sequence_mouse.pl:251
Date (localtime)    = Sat Mar  5 18:55:10 2016
Ensembl API version = 83

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