<div dir="ltr">Hi Yuan,<div><br></div><div>I don't see this error message - are you using the Sanger cache?</div><div><br></div><div>Which options are you using?</div><div><br></div><div>My output is below.</div><div><br>
</div><div>Regards</div><div><br></div><div>Will</div><div><br></div><div>> perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i yuan.vcf -cache -species gorilla -force -dir /data/blastdb/Ensembl/vep -everything -no_progress<br>
</div><div>2014-06-05 10:25:26 - Read existing cache info</div><div>2014-06-05 10:25:26 - Auto-detected FASTA file in cache directory</div><div>2014-06-05 10:25:26 - Checking/creating FASTA index</div><div>2014-06-05 10:25:26 - INFO: Database will be accessed when using --sift; consider using the complete cache containing sift data (see documentation for details)</div>
<div>2014-06-05 10:25:26 - INFO: Database will be accessed when using --polyphen; consider using the complete cache containing polyphen data (see documentation for details)</div><div>2014-06-05 10:25:26 - Starting...</div>
<div>2014-06-05 10:25:26 - INFO: --sift is not available for this species</div><div>2014-06-05 10:25:26 - INFO: --polyphen is not available for this species</div><div>2014-06-05 10:25:26 - Detected format of input file as vcf</div>
<div>2014-06-05 10:25:26 - Read 1 variants into buffer</div><div>2014-06-05 10:25:26 - Checking for existing variations</div><div>2014-06-05 10:25:26 - WARNING: Could not find variation cache for 11:91000001-92000000</div>
<div>2014-06-05 10:25:26 - Reading transcript data from cache and/or database</div><div>2014-06-05 10:25:26 - Retrieved 32 transcripts (0 mem, 32 cached, 0 DB, 0 duplicates)</div><div>2014-06-05 10:25:26 - Analyzing chromosome 11</div>
<div>2014-06-05 10:25:26 - Analyzing variants</div><div>2014-06-05 10:25:26 - Calculating consequences</div><div>2014-06-05 10:25:26 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)</div><div>2014-06-05 10:25:26 - Wrote stats summary to variant_effect_output.txt_summary.html</div>
<div>2014-06-05 10:25:26 - Finished!</div><div><br></div><div>> grep -v # variant_effect_output.txt</div><div><div>11_91630310_A/G 11:91630310 G ENSGGOG00000014840 ENSGGOT00000014893 Transcript missense_variant 55 55</div>
<div> 19 T/A Acc/Gcc - STRAND=1;SYMBOL=FOLR4;HGVSc=ENSGGOT00000014893.2:c.55A>G;DOMAINS=Pfam_domain:PF03024,Cleavage_site_(Signalp):Sigp;HGVSp=ENSGGOP00000014480.2:p.Thr19Ala;SYMBOL_SOURCE=Uniprot_gn;ENSP=ENSGGOP00000014480;EXON=1/4;BIOTYPE=protein_coding;CANONICAL=YES</div>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 June 2014 03:38, Yuan Chen <span dir="ltr"><<a href="mailto:yuan@sanger.ac.uk" target="_blank">yuan@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Will,<br>
<br>
I have a gorilla variant :<br>
11 91630310 . A G<br>
<br>
if I use species gorilla_gorilla, then I got error message :<br>
Can't call method "db" on unblessed reference at /nfs/team19/yuan/ensembl-checkout/ensembl-variation-75/modules/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 322, <GEN0> line 9<br>
<br>
if I use other species, such as homo_sapiens, then it’s fine with same config file, only species is different.<br>
WEB tool on gorilla runs fine as well.<br>
<br>
Could you help on this please.<br>
<span class="HOEnZb"><font color="#888888"><br>
yuan</font></span><br>_______________________________________________<br>
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<br></blockquote></div><br></div>