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Hi Michael,<br>
<br>
The values 'version' and 'sequence_level' are normally read found in
the coord_system table<br>
<br>
Example from our 75 database:<br>
<a class="moz-txt-link-abbreviated" href="mailto:anonymous@ensembldb.ensembl.org">anonymous@ensembldb.ensembl.org</a> : homo_sapiens_core_75_37 >select
* from coord_system ;<br>
+-----------------+------------+-------------+---------+------+--------------------------------+<br>
| coord_system_id | species_id | name | version | rank |
attrib |<br>
+-----------------+------------+-------------+---------+------+--------------------------------+<br>
| 1 | 1 | contig | NULL | 4 |
default_version,sequence_level |<br>
| 2 | 1 | chromosome | GRCh37 | 1 |
default_version |<br>
| 3 | 1 | supercontig | GRCh37 | 2 |
default_version |<br>
| 4 | 1 | clone | NULL | 3 |
default_version |<br>
+-----------------+------------+-------------+---------+------+--------------------------------+<br>
<br>
Can you check that your local database is correctly populated?<br>
I would expect this data to be found in the core database, as well
as the otherfeatures, rnaseq, cdna and vega ones.<br>
<br>
<br>
Hope that helps,<br>
mag<br>
<br>
<div class="moz-cite-prefix">On 10/08/2014 06:30, Michael Yourshaw
wrote:<br>
</div>
<blockquote
cite="mid:17276629-D762-4D5D-B336-6D6C4BCC4065@g.ucla.edu"
type="cite">
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In VEP version 75 I'm getting the warning "uninitialized value
$version” followed by the error “No sequence_level coord_system is
defined”).
<div><br>
</div>
<div>Might there be something wrong with my setup, which consists
of a local db installation and the downloaded cache?<br>
<div><br>
</div>
<div>Full transcript follows.<br>
<div><br>
</div>
<div>
<div>2014-08-09 17:18:51 - Read configuration from
/home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini</div>
<div>#----------------------------------#</div>
<div># ENSEMBL VARIANT EFFECT PREDICTOR #</div>
<div>#----------------------------------#</div>
<div><br>
</div>
<div>version 75</div>
<div><br>
</div>
<div>By Will McLaren (<a moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)</div>
<div><br>
</div>
<div>Configuration options:</div>
<div><br>
</div>
<div>allele_number 1</div>
<div>biotype 1</div>
<div>cache 1</div>
<div>canonical 1</div>
<div>ccds 1</div>
<div>check_alleles 1</div>
<div>check_existing 1</div>
<div>check_ref 1</div>
<div>check_svs 1</div>
<div>config
/home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini</div>
<div>core_type core</div>
<div>database 1</div>
<div>dir /share/apps/myourshaw/vax/vep_cache</div>
<div>dir_cache /share/apps/myourshaw/vax/vep_cache</div>
<div>dir_plugins /share/apps/myourshaw/vax/Plugins</div>
<div>domains 1</div>
<div>force_overwrite 1</div>
<div>gene 1</div>
<div>gmaf 1</div>
<div>hgvs 1</div>
<div>host cortex.local</div>
<div>input_file
/scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf</div>
<div>maf_1kg 1</div>
<div>maf_esp 1</div>
<div>no_progress 1</div>
<div>numbers 1</div>
<div>output_file
/scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf.vax</div>
<div>password xxx</div>
<div>polyphen b</div>
<div>port 3306</div>
<div>protein 1</div>
<div>pubmed 1</div>
<div>regulatory 1</div>
<div>sift b</div>
<div>species homo_sapiens</div>
<div>stats HASH(0x6665860)</div>
<div>symbol 1</div>
<div>terms SO</div>
<div>user xxx</div>
<div>verbose 1</div>
<div>xref_refseq 0</div>
<div><br>
</div>
<div>--------------------</div>
<div><br>
</div>
<div>Will only load v75 databases</div>
<div>Species 'homo_sapiens' loaded from database
'homo_sapiens_core_75_37'</div>
<div>Species 'homo_sapiens' loaded from database
'homo_sapiens_cdna_75_37'</div>
<div>Species 'homo_sapiens' loaded from database
'homo_sapiens_vega_75_37'</div>
<div>Species 'homo_sapiens' loaded from database
'homo_sapiens_otherfeatures_75_37'</div>
<div>Species 'homo_sapiens' loaded from database
'homo_sapiens_rnaseq_75_37'</div>
<div>homo_sapiens_variation_75_37 loaded</div>
<div>homo_sapiens_funcgen_75_37 loaded</div>
<div>ensembl_compara_75 loaded</div>
<div>ensembl_ancestral_75 loaded</div>
<div>ensembl_ontology_75 loaded</div>
<div>No production database or adaptor found</div>
<div>ensembl_stable_ids_75 loaded</div>
<div>2014-08-09 17:19:18 - Connected to core version 75
database and variation version 75 database</div>
<div>2014-08-09 17:19:18 - Read existing cache info</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>Use of uninitialized value $version in concatenation
(.) or string at
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
line 304.</div>
<div>2014-08-09 17:22:42 - INFO: Database will be accessed
when using --hgvs</div>
<div>2014-08-09 17:22:42 - INFO: Database will be accessed
when using --check_ref</div>
<div>2014-08-09 17:22:42 - Starting...</div>
<div>2014-08-09 17:22:42 - Detected format of input file as
vcf</div>
<div><br>
</div>
<div>-------------------- EXCEPTION --------------------</div>
<div>MSG: No sequence_level coord_system is defined</div>
<div>STACK
Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_sequence_level
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm:631</div>
<div>STACK
Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_Slice_start_end_strand
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm:246</div>
<div>STACK Bio::EnsEMBL::Slice::seq
/share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/Slice.pm:655</div>
<div>STACK Bio::EnsEMBL::Variation::Utils::VEP::validate_vf
/share/apps/myourshaw/vax/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:2844</div>
<div>STACK main::main
/home/myourshaw/lab/pypeline/vax/vep.pl:289</div>
<div>STACK toplevel
/home/myourshaw/lab/pypeline/vax/vep.pl:172</div>
<div>Date (localtime) = Sat Aug 9 17:23:17 2014</div>
<div>Ensembl API version = 75</div>
<div>---------------------------------------------------</div>
</div>
</div>
</div>
<div><br>
</div>
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