<div dir="ltr">Hello Alan,<div><br></div><div>Thanks for the detailed report. There's an odd bug happening here which I can't get to the bottom of at the moment.</div><div><br></div><div>I've added a fix for now which stops the error happening, and the cache builds fine for me from your input.</div>
<div><br></div><div>Since we're in the process of switching our code hosting to Git, for now I have only pushed the fix to our GitHub - you can get the fixed script here:</div><div><br></div><div><a href="https://github.com/Ensembl/ensembl-tools/blob/release/74/scripts/variant_effect_predictor/gtf2vep.pl">https://github.com/Ensembl/ensembl-tools/blob/release/74/scripts/variant_effect_predictor/gtf2vep.pl</a></div>
<div><br></div><div>Let me know if this isn't convenient and I can get the fix pushed to our CVS tree too.</div><div><br></div><div>PS I assume you are aware we build a cache file for macaque already? <a href="ftp://ftp.ensembl.org/pub/release-74/variation/VEP/">ftp://ftp.ensembl.org/pub/release-74/variation/VEP/</a></div>
<div><br></div><div>Thanks again</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 8 January 2014 05:38, Harris, Ronald Alan <span dir="ltr"><<a href="mailto:rharris1@bcm.edu" target="_blank">rharris1@bcm.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:x-small;font-family:Tahoma">
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<div dir="ltr"><font color="#000000" face="Tahoma">Hi,</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I have been trying to use <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a><a></a> to generate a cache file based on RhesusBase<a></a> (<a href="http://www.rhesusbase.org/" target="_blank">http://www.rhesusbase.org/</a>) gene annotations on the UCSC<a></a> rheMac2<a></a>/Ensembl<a></a> MMUL_1<a></a>
assembly. I downloaded their rb2<a></a> gene predictions as a gtf<a></a> file through their UCSC<a></a> mirror, changed the source column to "protein_coding<a></a>", added "exon_number<a></a>" and the appropriate number in the description field, and sorted
the annotations by chromosome position. The gtf<a></a> file can be downloaded from here:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><a href="https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu" target="_blank">https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu</a></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">When I run <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a><a></a> I get this error:</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Can't call method "start" on an undefined value at <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a><a></a> line 376.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">This error occurs after generating some of the cache files in the .vep<a></a> directory. I tried to run <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a><a></a> using gtf<a></a> files with only a single chromosome and it looks like the error consistently occurs
when trying to generate the 1-1000000 cache file. Oddly, if I just run <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a><a></a> on the annotations from 1-1000000 on a single chromosome I do not get this error.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I don't think this is due to chr<a></a> in chromosome names because the fasta<a></a> file I am using has chr<a></a> in the chromosome names.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">I would appreciate any help you could give me with this.</font></div>
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Thanks,</font></div><span class="HOEnZb"><font color="#888888">
<div dir="ltr"><font face="tahoma"></font> </div>
<div dir="ltr"><font face="tahoma">Alan</font></div>
</font></span></div>
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<br></blockquote></div><br></div>