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

[Pierre Lindenbaum]

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