<div dir="ltr"><div>Hi again,</div><div><br></div>We've patched in a fix for this that should prevent the script from exiting when encountering this scenario; again if you re-run INSTALL.pl and re-install the API you should get the fix.<div><br></div><div>There is still an outstanding problem here, as the consequence type field for the particular variant type that causes this issue will be left blank.</div><div><br></div><div>We're working on a complete fix for this that should be ready in the coming days.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 20 March 2015 at 08:55, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello again,<div><br></div><div>VEP.pm does not contain the impact() function itself, but it does refer to objects on which that method may be called (if you're interested you'll find the method in OverlapConsequence.pm).</div><div><br></div><div>If you're still seeing the same error as above, it would be useful to help us debug the problem if you could provide a line or two of input from your VCF (or other input file) that recreates the error message.</div><div><br></div><div>Thanks for the feedback</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 19 March 2015 at 23:21, namchul ghim <span dir="ltr"><<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thank you for your reponse.<div><br></div><div>I ran <a href="http://INSTALL.PL" target="_blank">INSTALL.PL</a> again twice.</div><div><br></div><div>but, VEP.pm doesn't contain impact() function still.</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 18, 2015 at 6:27 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>The error you report is a bug that was fixed a couple of days ago; if you update your API code (either re-run INSTALL.pl or use "git pull" in the ensembl-variation directory if you installed the API from GitHub) you should no longer see this error.</div><div><br></div><div>The warning messages you see are because your input chromosome coordinates are not valid for build GRCh38; note the difference in chromosome length for chr22 between GRCh38:</div><div><br></div><div><a href="http://www.ensembl.org/Homo_sapiens/Location/Chromosome?r=22" target="_blank">http://www.ensembl.org/Homo_sapiens/Location/Chromosome?r=22</a><br></div><div><br></div><div>and GRCh37</div><div><br></div><div><a href="http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=22" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=22</a><br></div><div><br></div><div>You should only use input files that have been called against or remapped to GRCh38 when using the GRCh38 cache; the VEP does NOT do any remapping for you. If you wish to remap your data from GRCh37 to GRCh38, you can try the Assembly Converter tool - it comes as part of the ensembl-tools package, or you can use it online here: <a href="http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core" target="_blank">http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core</a><br></div><div><br></div><div>Regards</div><span><font color="#888888"><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></font></span></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On 18 March 2015 at 07:32, namchul ghim <span dir="ltr"><<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div style="font-size:12.8000001907349px">After installing Ensembl_v79, I annotated vep cache with GRch37. </div><div style="font-size:12.8000001907349px">When doing so I got a following message: <br>Can't call method "impact" on an undefined value at /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor <br>/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">When I checked the following source file, there is no definition of imapct() function. There is only function name in the same line.</div><div style="font-size:12.8000001907349px">Isn't that a bug?</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Also, in same condition, annotating only vep cache with GRCh38 version was successful.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">What is going on?</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Additionally, when I was annotating vep cache with GRCh38 version, there is a warning message in cache file.</div><div style="font-size:12.8000001907349px">The warning message is as follow:</div><span style="font-size:12.8000001907349px"><div>WARNING: Could not find variation cache for 22:51000001-52000000</div><div>WARNING: Could not find variation cache for 22:51000001-52000000</div><div>WARNING: Could not find variation cache for 22:51000001-52000000</div><div>WARNING: Could not find variation cache for 22:51000001-52000000</div><div>WARNING: Could not find cache for 22:51000001-52000000</div><div>WARNING: Could not find cache for 22:51000001-52000000</div><div><br></div></span><div style="font-size:12.8000001907349px">When I checked the actual cache folder, there is no file in such range. Is this something I should consider or can I ignore this message?</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">For your information, the vep cahce is downloaded in this location:</div><div style="font-size:12.8000001907349px"><a href="ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz</a></div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Thank you very much!</div></div>
<br></div></div><span>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></span></blockquote></div><br></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>
</div></div></blockquote></div><br></div>