<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><br></div><div><br></div><div><b>TERMINAL OUTPUT (forking off):</b></div><div><div><div><div>compute-4-46:myourshaw$ /home/myourshaw/apps/ActivePerl-5.16/bin/perl /share/apps/myourshaw/vax/vax.pl -input_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf -output_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.vcf.vax --config /share/apps/myourshaw/vax/vep_lite.ini</div><div>2012-12-30 16:57:53 - 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_37053338.vcf</div><div>no_progress 1</div><div>numbers 1</div><div>output_file /scratch0/tmp/myourshaw/00000928.3.00-All.vcf.gz.vex_37053338.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>2012-12-30 16:57:53 - Connected to core version 69 database and variation version 69 database</div><div>2012-12-30 16:57:53 - Loaded plugin: vw</div><div>2012-12-30 16:57:53 - Loaded plugin: Condel</div><div>2012-12-30 16:57:53 - Loaded plugin: VCFCols</div><div>2012-12-30 16:57:53 - Fetching regulatory features for plugin: VCFCols</div><div>2012-12-30 16:57:53 - Loaded plugin: ExtraCols</div><div>2012-12-30 16:57:53 - Fetching regulatory features for plugin: ExtraCols</div><div>2012-12-30 16:57:53 - Loaded plugin: Consequences</div><div>2012-12-30 16:57:53 - Fetching regulatory features for plugin: Consequences</div><div>2012-12-30 16:57:53 - Loaded plugin: Conservation</div><div>2012-12-30 16:57:53 - Fetching regulatory features for plugin: Conservation</div><div>2012-12-30 16:57:53 - Starting...</div><div>2012-12-30 16:57:53 - Read 1 variants into buffer</div><div>2012-12-30 16:57:53 - Reading transcript data from cache and/or database</div><div>2012-12-30 16:57:53 - Retrieved 23 transcripts (0 mem, 0 cached, 23 DB, 0 duplicates)</div><div>2012-12-30 16:57:53 - Reading regulatory data from cache and/or database</div><div>2012-12-30 16:57:53 - Retrieved 1 regulatory features (0 mem, 0 cached, 1 DB, 0 duplicates)</div><div>2012-12-30 16:57:53 - Checking for existing variations</div><div>2012-12-30 16:57:53 - Checking for overlapping structural variations</div><div>2012-12-30 16:57:53 - Analyzing chromosome 3</div><div>2012-12-30 16:57:53 - Analyzing variants</div><div>2012-12-30 16:57:53 - Analyzing RegulatoryFeatures</div><div>2012-12-30 16:57:53 - Calculating consequences</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 923, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 927, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 945, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 959, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 963, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 756, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 772, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 809, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 828, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 923, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 927, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 945, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 959, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 963, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 756, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 772, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 809, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 828, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 923, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 927, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 945, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 959, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 963, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 756, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 772, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 809, <GEN1> line 60.</div><div>Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 828, <GEN1> line 60.</div><div>2012-12-30 16:57:54 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)</div><div>2012-12-30 16:57:54 - Finished!</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" 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 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