<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all<div><br></div><div>I am trying to run vep script using local database and cache using the following command.</div><div><br></div><div>perl variant_effect_predictor.pl --output_file output.vep --species homo_sapiens --host localhost --user user --password password --port 1111 --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift b --force_overwrite --input_file input.vcf -skip_db_check</div><div><br></div><div><br></div><div>However, there are few warning thrown. Could somebody please let me know if these warnings are acceptable and will not affect the output in anyways?</div><div><br></div><div>First warning:</div><div><div>Use of qw(...) as parentheses is deprecated at /home/depressed/variant_effect_predictor/variant_effect_predictor.pl line 848.</div></div><div><br></div><div>I am guessing this is the result of using perl v14.2 and also guessing that this should not have any serious consequence at this stage.</div><div><br></div><div>Second warning is as follows:</div><div>2012-01-26 17:11:42 - Reading cached adaptor data</div><div><div>Use of uninitialized value in join or string at /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 3495.</div></div><div><br></div><div>Again guessing that this doesn't cascade into serious trouble while reporting results of the script.</div><div><br></div><div>However I am more concerned about following warnings (I get multiple of them).</div><div><br></div><div>Use of uninitialized value in sprintf at /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 932, <GEN0> line 315932.</div><div><br></div><div>Trying to debug the code indicated that vcf line responsible for these are (examples only out of many)</div><div><br></div><div><div>chr1<span class="Apple-tab-span" style="white-space:pre"> </span>57005269<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>AACACA<span class="Apple-tab-span" style="white-space:pre"> </span>AACA<span class="Apple-tab-span" style="white-space:pre"> </span>217<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>INDEL;DP=25;VDB=0.0292;AF1=0.5;AC1=1;DP4=9,5,4,6;MQ=50;FQ=217;PV4=0.41,0.00046,1,0.38<span class="Apple-tab-span" style="white-space:pre"> </span>GT:PL:DP:SP:GQ<span class="Apple-tab-span" style="white-space:pre"> </span>0/1:255,0,255:24:4:99</div></div><div>chr1<span class="Apple-tab-span" style="white-space:pre"> </span>61542770<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>GAGGGGAGAAGGGG<span class="Apple-tab-span" style="white-space:pre"> </span>GAGGGGAGAAGGGGAGAAGGGG<span class="Apple-tab-span" style="white-space:pre"> </span>106<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>INDEL;DP=23;VDB=0.0337;AF1=0.5;AC1=1;DP4=1,9,3,6;MQ=41;FQ=109;PV4=0.3,1,0,1<span class="Apple-tab-span" style="white-space:pre"> </span>GT:PL:DP:SP:GQ<span class="Apple-tab-span" style="white-space:pre"> </span>0/1:144,0,245:19:5:99</div><div><div><br></div><div>Any help on this matter is greatly appreciated.</div><div><br></div><div>Thanking you.</div><div><br></div><div>Kind regards</div><div><br></div><div><br></div><div apple-content-edited="true">
<div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="'Helvetica Neue'"><b>Hardip R. Patel, PhD</b></font></div><div><font class="Apple-style-span" face="'Helvetica Neue'"><i>Post-doctoral Research Fellow</i></font></div><div><font class="Apple-style-span" face="'Helvetica Neue'"><br></font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">Genome Discovery Unit and RNA Biology Lab</font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">Genome Biology Department</font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">The John Curtin School of Medical Research</font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">College of Medicine, Biology and Environment</font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">The Australian National University</font></div></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="'Helvetica Neue'">Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia</font></div></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span" face="'Helvetica Neue'">Email: <a href="mailto:hardip.patel@anu.edu.au">hardip.patel@anu.edu.au</a>, <a href="mailto:patelhardip@gmail.com">patelhardip@gmail.com</a></font></div><div><font class="Apple-style-span" face="'Helvetica Neue'">Phone Number: (+61) 0449 180 715</font></div><div style="font-family: Courier; font-size: medium; font-weight: normal; font-style: normal; "><br></div></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline">
</div>
<br></div></body></html>