<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; "><div><div><div></div><div><br></div><div><b>TERMINAL OUTPUT:</b></div><div><div>2012-12-31 12:10:07 - Read configuration from /share/apps/myourshaw/vax/vep_lite.ini</div><div>#----------------------------------#</div><div># ENSEMBL VARIANT EFFECT PREDICTOR #</div><div>#----------------------------------#</div><div><br></div><div>version 2.7</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> </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 /share/apps/myourshaw/vax/vep_lite.ini</div><div>core_type core</div><div>dir /home/myourshaw/.vep</div><div>domains 1</div><div>force_overwrite 1</div><div>format vcf</div><div>gene 1</div><div>gmaf 1</div><div>hgnc 1</div><div>hgvs 1</div><div>host cortex.local</div><div>input_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37061804.vcf</div><div>no_progress 1</div><div>numbers 1</div><div>output_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37061804.vcf.vax</div><div>password ensembl</div><div>plugin vw<span class="Apple-tab-span" style="white-space:pre"> </span>Condel,/share/apps/myourshaw/VEP_plugins/config/Condel/config,b,2<span class="Apple-tab-span" style="white-space:pre"> </span>VCFCols<span class="Apple-tab-span" style="white-space:pre"> </span>ExtraCols<span class="Apple-tab-span" style="white-space:pre"> </span>Consequences<span class="Apple-tab-span" style="white-space:pre"> </span>Conservation</div><div>polyphen b</div><div>port 3306</div><div>protein 1</div><div>regulatory 1</div><div>sift b</div><div>species homo_sapiens</div><div>terms SO</div><div>toplevel_dir /home/myourshaw/.vep</div><div>user ensembl</div><div>verbose 0</div><div>xref_refseq 1</div><div><br></div><div>--------------------</div><div><br></div><div>2012-12-31 12:10:07 - Connected to core version 69 database and variation version 69 database</div><div>2012-12-31 12:10:07 - Loaded plugin: vw</div><div>2012-12-31 12:10:07 - Loaded plugin: Condel</div><div>2012-12-31 12:10:07 - Loaded plugin: VCFCols</div><div>2012-12-31 12:10:07 - Fetching regulatory features for plugin: VCFCols</div><div>2012-12-31 12:10:07 - Loaded plugin: ExtraCols</div><div>2012-12-31 12:10:07 - Fetching regulatory features for plugin: ExtraCols</div><div>2012-12-31 12:10:07 - Loaded plugin: Consequences</div><div>2012-12-31 12:10:07 - Fetching regulatory features for plugin: Consequences</div><div>2012-12-31 12:10:09 - Loaded plugin: Conservation</div><div>2012-12-31 12:10:09 - Fetching regulatory features for plugin: Conservation</div><div>2012-12-31 12:10:09 - Starting...</div><div>2012-12-31 12:10:09 - Read 1 variants into buffer</div><div>2012-12-31 12:10:09 - Reading transcript data from cache and/or database</div><div>2012-12-31 12:10:09 - Retrieved 23 transcripts (0 mem, 0 cached, 23 DB, 0 duplicates)</div><div>2012-12-31 12:10:09 - Reading regulatory data from cache and/or database</div><div>2012-12-31 12:10:10 - Retrieved 3 regulatory features (0 mem, 0 cached, 3 DB, 0 duplicates)</div><div>2012-12-31 12:10:10 - Checking for existing variations</div><div>2012-12-31 12:10:10 - Checking for overlapping structural variations</div><div>2012-12-31 12:10:10 - Analyzing chromosome 3</div><div>2012-12-31 12:10:10 - Analyzing variants</div><div>2012-12-31 12:10:10 - Analyzing RegulatoryFeatures</div><div>2012-12-31 12:10:10 - Analyzing MotifFeatures</div><div>2012-12-31 12:10:10 - Calculating consequences</div><div>Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 865, <GEN2> line 60.</div></div><div><br></div><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; font-size: 12px; border-spacing: 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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -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-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal '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-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.</span></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></span>
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