Hi Pierre,<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>Thanks</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation<br><br><div class="gmail_quote">On 25 February 2011 09:30, Pierre Lindenbaum <span dir="ltr"><<a href="mailto:pierre.lindenbaum@univ-nantes.fr">pierre.lindenbaum@univ-nantes.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">hi Ensembl,<br>
<br>
I've downloaded a fresh version of <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> and I'm running it this way:<br>
<br>
cat *.vcf | cut -d ' ' -f 1-5 | sort | uniq | ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --format vcf -o ~/variant_effect_out.txt --check_ref --hgnc<br>
<br>
for a few hours nothing happens (variant_effect_out.txt remains empty )<br>
<br>
and then, the program raises the following error:<br>
<br>
Could not connect to database homo_sapiens_core_61_37f as user anonymous using [DBI:mysql:database=homo_sapiens_core_61_37f;host=<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>;port=5306] as a locator:<br>
Can't connect to MySQL server on '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>' (110) at /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 290, <STDIN> line 500.<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Could not connect to database homo_sapiens_core_61_37f as user anonymous using [DBI:mysql:database=homo_sapiens_core_61_37f;host=<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>;port=5306] as a locator:<br>
Can't connect to MySQL server on '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>' (110)<br>
STACK Bio::EnsEMBL::DBSQL::DBConnection::connect /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:299<br>
STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:618<br>
STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:647<br>
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:164<br>
STACK Bio::EnsEMBL::DBSQL::AttributeAdaptor::fetch_all_by_ /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm:282<br>
STACK Bio::EnsEMBL::DBSQL::AttributeAdaptor::AUTOLOAD /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm:100<br>
STACK Bio::EnsEMBL::Slice::get_all_Attributes /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:1237<br>
STACK Bio::EnsEMBL::Slice::is_circular /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:536<br>
STACK Bio::EnsEMBL::Slice::project /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:881<br>
STACK Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_Slice_start_end_strand /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm:220<br>
STACK Bio::EnsEMBL::Slice::subseq /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Slice.pm:642<br>
STACK Bio::EnsEMBL::Exon::seq /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Exon.pm:1467<br>
STACK Bio::EnsEMBL::Transcript::spliced_seq /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:768<br>
STACK Bio::EnsEMBL::Transcript::translateable_seq /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:824<br>
STACK Bio::EnsEMBL::Transcript::translate /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Transcript.pm:1655<br>
STACK Bio::EnsEMBL::Utils::TranscriptAlleles::type_variation /home/lindenb/tmp/ENSEMBL/ensembl/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm:289<br>
STACK Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::_calc_consequences /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm:586<br>
STACK Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor::fetch_all_by_VariationFeatures /home/lindenb/tmp/ENSEMBL/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm:442<br>
STACK toplevel ./<a href="http://variant_effect_predictor.pl:356" target="_blank">variant_effect_predictor.pl:356</a><br>
Ensembl API version = 61<br>
<br>
<br>
Note that I can connect to this database from the very same computer:<br>
<br>
mysql -u anonymous -h <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a> -P 5306 -D homo_sapiens_core_61_37f -A -e 'select * from xref limit 1'<br>
+---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+<br>
| xref_id | external_db_id | dbprimary_acc | display_label | version | description | info_type | info_text |<br>
+---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+<br>
| 8492626 | 1810 | NP_001185689 | NP_001185689.1 | 1 | LY75-CD302 fusion protein isoform 2 precursor | SEQUENCE_MATCH | NULL |<br>
+---------+----------------+---------------+----------------+---------+------------------------------------------------+----------------+-----------+<br>
<br>
If I only use the 3 first rows, the program returns successfully:<br>
<br>
cat *.vcf | sort | uniq | head -n 3 | ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --format vcf -o ~/variant_effect_out.txt --check_ref --hgnc<br>
<br>
wc ~/variant_effect_out.txt<br>
7 71 591 /home/lindenb/variant_effect_out.txt<br>
<br>
<br>
Thanks for your help<br>
<br>
Pierre Lindenbaum<br>
<br>
<br>
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</blockquote></div><br></div>