<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">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 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><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><span class="Apple-style-span" style="border-collapse: separate; font-family: 'Lucida Grande'; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 10px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><p class="MsoNormal"><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px;"><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br class="Apple-interchange-newline"></span></font><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px;">ॐ</span></font></span></font></p></span><p></p><p style="margin: 0px 0px 6px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-family: Helvetica;"><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px;">Michael Yourshaw, PhD</span></p><div style="margin: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">UCLA Geffen School of Medicine</span></div><div style="margin: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">Department of Pediatrics</span></div><div style="margin: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">695 Charles E Young Drive S</span></div><div style="margin: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">Gonda 5554</span></div><p style="margin: 0px 0px 3px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">Los Angeles CA 90095-8348 USA</span></p><p style="margin: 0px 0px 3px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande'; color: rgb(0, 0, 153);"><span style="text-decoration: underline; letter-spacing: 0px;"><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin: 0px 0px 6px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">970.691.8299</span></p><p style="margin: 0px 0px 6px; font-style: normal; font-variant: normal; font-weight: normal; font-size: 9px; line-height: normal; font-family: 'Lucida Grande';"><span style="letter-spacing: 0px;">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</span> do not read, copy, or forward this message or any attachments. Please permanently<span style="letter-spacing: 0px;"> delete all copies of the message and any attachments and notify the sender immediately by sending an email to <a href="mailto:myourshaw@yourshaw.org">myourshaw@yourshaw.org</a>. Thank you. As part of our </span>commitment<span style="letter-spacing: 0px;"> to the environment, this </span>message was manufactured with 100% recycled electrons.</p><div><font class="Apple-style-span" size="1"><span class="Apple-style-span" style="font-size: 9px;"><br></span></font></div></span><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></span></div></span></div></div>
</div>
<br></body></html>