[ensembl-dev] VEP error “No sequence_level coord_system is defined”
Michael Yourshaw
myourshaw at g.ucla.edu
Mon Aug 11 19:55:43 BST 2014
Thanks for the quick answer. It turned out I was missing the “contig” record due to a faulty mysqlimport command.
You guys are great!
ॐ
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
970.691.8299
This message (including any attachments) is intended only for the use of the addressee(s) and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may constitute ATTORNEY WORK PRODUCT. If you are not an intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this message in error, please do not read, copy, or forward this message or any attachments. Please permanently delete all copies of the message and any attachments and notify the sender immediately by sending an email to myourshaw at yourshaw.org. Thank you. As part of our commitment to the environment, this message was manufactured with 100% recycled electrons.
On Aug 11, 2014, at 05:38, mag <mr6 at ebi.ac.uk> wrote:
> 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)
>>
>> 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
>> ---------------------------------------------------
>>
>>
>> ॐ
>>
>> 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
>> 970.691.8299
>>
>> This message (including any attachments) is intended only for the use of the addressee(s) and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may constitute ATTORNEY WORK PRODUCT. If you are not an intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this message in error, please do not read, copy, or forward this message or any attachments. Please permanently delete all copies of the message and any attachments and notify the sender immediately by sending an email to myourshaw at yourshaw.org. Thank you. As part of our commitment to the environment, this message was manufactured with 100% recycled electrons.
>>
>>
>>
>>
>>
>>
>>
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