[ensembl-dev] VEP error “No sequence_level coord_system is defined”
mag
mr6 at ebi.ac.uk
Mon Aug 11 13:38:57 BST 2014
Hi Michael,
The values 'version' and 'sequence_level' are normally read found in the
coord_system table
Example from our 75 database:
anonymous at ensembldb.ensembl.org : homo_sapiens_core_75_37 >select * from
coord_system ;
+-----------------+------------+-------------+---------+------+--------------------------------+
| coord_system_id | species_id | name | version | rank |
attrib |
+-----------------+------------+-------------+---------+------+--------------------------------+
| 1 | 1 | contig | NULL | 4 |
default_version,sequence_level |
| 2 | 1 | chromosome | GRCh37 | 1 |
default_version |
| 3 | 1 | supercontig | GRCh37 | 2 |
default_version |
| 4 | 1 | clone | NULL | 3 |
default_version |
+-----------------+------------+-------------+---------+------+--------------------------------+
Can you check that your local database is correctly populated?
I would expect this data to be found in the core database, as well as
the otherfeatures, rnaseq, cdna and vega ones.
Hope that helps,
mag
On 10/08/2014 06:30, Michael Yourshaw wrote:
> In VEP version 75 I'm getting the warning "uninitialized value
> $version” followed by the error “No sequence_level coord_system is
> defined”).
>
> Might there be something wrong with my setup, which consists of a
> local db installation and the downloaded cache?
>
> Full transcript follows.
>
> 2014-08-09 17:18:51 - Read configuration from
> /home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini
> #----------------------------------#
> # ENSEMBL VARIANT EFFECT PREDICTOR #
> #----------------------------------#
>
> version 75
>
> By Will McLaren (wm2 at ebi.ac.uk <mailto:wm2 at ebi.ac.uk>)
>
> Configuration options:
>
> allele_number 1
> biotype 1
> cache 1
> canonical 1
> ccds 1
> check_alleles 1
> check_existing 1
> check_ref 1
> check_svs 1
> config /home/myourshaw/lab/pypeline/vax/75/vep_no_plugins.ini
> core_type core
> database 1
> dir /share/apps/myourshaw/vax/vep_cache
> dir_cache /share/apps/myourshaw/vax/vep_cache
> dir_plugins /share/apps/myourshaw/vax/Plugins
> domains 1
> force_overwrite 1
> gene 1
> gmaf 1
> hgvs 1
> host cortex.local
> input_file
> /scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf
> maf_1kg 1
> maf_esp 1
> no_progress 1
> numbers 1
> output_file
> /scratch1/tmp/myourshaw/rnaseq_20140227/vcfs/gatk/rnaseq_20140227.hc.analysis_ready.vcf.vax
> password xxx
> polyphen b
> port 3306
> protein 1
> pubmed 1
> regulatory 1
> sift b
> species homo_sapiens
> stats HASH(0x6665860)
> symbol 1
> terms SO
> user xxx
> verbose 1
> xref_refseq 0
>
> --------------------
>
> Will only load v75 databases
> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_75_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_75_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_75_37'
> Species 'homo_sapiens' loaded from database
> 'homo_sapiens_otherfeatures_75_37'
> Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_75_37'
> homo_sapiens_variation_75_37 loaded
> homo_sapiens_funcgen_75_37 loaded
> ensembl_compara_75 loaded
> ensembl_ancestral_75 loaded
> ensembl_ontology_75 loaded
> No production database or adaptor found
> ensembl_stable_ids_75 loaded
> 2014-08-09 17:19:18 - Connected to core version 75 database and
> variation version 75 database
> 2014-08-09 17:19:18 - Read existing cache info
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> Use of uninitialized value $version in concatenation (.) or string at
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
> line 304.
> 2014-08-09 17:22:42 - INFO: Database will be accessed when using --hgvs
> 2014-08-09 17:22:42 - INFO: Database will be accessed when using
> --check_ref
> 2014-08-09 17:22:42 - Starting...
> 2014-08-09 17:22:42 - Detected format of input file as vcf
>
> -------------------- EXCEPTION --------------------
> MSG: No sequence_level coord_system is defined
> STACK Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_sequence_level
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm:631
> STACK
> Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_Slice_start_end_strand
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm:246
> STACK Bio::EnsEMBL::Slice::seq
> /share/apps/myourshaw/vax/ensembl/ensembl/modules/Bio/EnsEMBL/Slice.pm:655
> STACK Bio::EnsEMBL::Variation::Utils::VEP::validate_vf
> /share/apps/myourshaw/vax/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:2844
> STACK main::main /home/myourshaw/lab/pypeline/vax/vep.pl:289
> STACK toplevel /home/myourshaw/lab/pypeline/vax/vep.pl:172
> Date (localtime) = Sat Aug 9 17:23:17 2014
> Ensembl API version = 75
> ---------------------------------------------------
>
>
> ?
>
> Michael Yourshaw, PhD
>
> UCLA Geffen School of Medicine
> Department of Pediatrics
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu <mailto:myourshaw at ucla.edu>
>
> 970.691.8299
>
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