[ensembl-dev] variant_effect_predictor.pl "Could not connect to database homo_sapiens_core_61_37f "

[Will McLaren]

Hi Pierre,

I would try running the script at first with a small file containing only a
few lines (10 or so) from your VCF, since sometimes the connection to our DB
server can time out after a while.

If you have a very large amount of data, you can also try running the script
in whole-genome mode - please refer to the README file that comes with the
script for guidance before doing this. You may also want to disable the
--check_ref and --hgnc flags as these can significantly increase the runtime
of the script.

Thanks

Will McLaren
Ensembl Variation

On 25 February 2011 09:30, Pierre Lindenbaum <
pierre.lindenbaum at univ-nantes.fr> wrote:

> hi Ensembl,
>
> I've downloaded a fresh version of variant_effect_predictor.pl and I'm
> running it this way:
>
> cat  *.vcf | cut -d '   ' -f 1-5 | sort | uniq | ./
> variant_effect_predictor.pl  --format vcf -o ~/variant_effect_out.txt
> --check_ref --hgnc
>
> for a few hours nothing happens (variant_effect_out.txt remains empty )
>
> and then, the program raises the following error:
>
>    Could not connect to database homo_sapiens_core_61_37f as user anonymous
> using [DBI:mysql:database=homo_sapiens_core_61_37f;host=
> ensembldb.ensembl.org;port=5306] as a locator:
>    Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
> line 290, <STDIN> line 500.
>
>    -------------------- EXCEPTION --------------------
>    MSG: Could not connect to database homo_sapiens_core_61_37f as user
> anonymous using [DBI:mysql:database=homo_sapiens_core_61_37f;host=
> ensembldb.ensembl.org;port=5306] as a locator:
>    Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
>    STACK Bio::EnsEMBL::DBSQL::DBConnection::connect
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:299
>    STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:618
>    STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:647
>    STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:164
>    STACK Bio::EnsEMBL::DBSQL::AttributeAdaptor::fetch_all_by_
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm:282
>    STACK Bio::EnsEMBL::DBSQL::AttributeAdaptor::AUTOLOAD
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm:100
>    STACK Bio::EnsEMBL::Slice::get_all_Attributes
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:1237
>    STACK Bio::EnsEMBL::Slice::is_circular
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:536
>    STACK Bio::EnsEMBL::Slice::project
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:881
>    STACK
> Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_Slice_start_end_strand
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm:220
>    STACK Bio::EnsEMBL::Slice::subseq
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:642
>    STACK Bio::EnsEMBL::Exon::seq
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Exon.pm:1467
>    STACK Bio::EnsEMBL::Transcript::spliced_seq
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:768
>    STACK Bio::EnsEMBL::Transcript::translateable_seq
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:824
>    STACK Bio::EnsEMBL::Transcript::translate
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:1655
>    STACK Bio::EnsEMBL::Utils::TranscriptAlleles::type_variation
> /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm:289
>    STACK
> Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::_calc_consequences
> /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm:586
>    STACK
> Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::fetch_all_by_VariationFeatures
> /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm:442
>    STACK toplevel ./variant_effect_predictor.pl:356
>    Ensembl API version = 61
>
>
> Note that I can connect to this database from the very same computer:
>
>  mysql -u anonymous -h ensembldb.ensembl.org -P 5306 -D
> homo_sapiens_core_61_37f -A -e 'select * from xref limit 1'
>
> +---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+
> | xref_id | external_db_id | dbprimary_acc | display_label  | version |
> description                                    | info_type      | info_text
> |
>
> +---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+
> | 8492626 |           1810 | NP_001185689  | NP_001185689.1 | 1       |
> LY75-CD302 fusion protein isoform 2 precursor  | SEQUENCE_MATCH | NULL
>  |
>
> +---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+
>
> If I only use the 3 first rows, the program returns successfully:
>
> cat *.vcf  | sort | uniq | head -n 3 | ./variant_effect_predictor.pl --format vcf -o ~/variant_effect_out.txt --check_ref --hgnc
>
> wc ~/variant_effect_out.txt
>  7  71 591 /home/lindenb/variant_effect_out.txt
>
>
> Thanks for your help
>
> Pierre Lindenbaum
>
>
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