<div dir="ltr">Hi Yuan,<div><br></div><div>SIFT is not available for gorilla. Currently supported species are:</div><br>Chicken, Cow, Dog, Human, Mouse, Pig, Rat and Zebrafish<br><br>If you remove sift from your options then it should work fine. However, the code should warn and continue gracefully; there is a bug in the script that I will fix.<br>
<br>Cheers<div><font color="#555555" face="Luxi Sans, Helvetica, Arial, Geneva, sans-serif"><span style="line-height:16px"><br></span></font></div><div><font color="#555555" face="Luxi Sans, Helvetica, Arial, Geneva, sans-serif"><span style="line-height:16px">Will</span></font></div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 6 June 2014 06:45, 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">
<div style="word-wrap:break-word">Yes, I am using Sanger cache, the config_file is : /lustre/scratch113/projects/g1k-fig/Gorilla/gorilla_ref/vcf_file/VEP/vep_config_file<div><br></div><div>If I use your way, it works it doesn’t matter whether I put -species gorilla or gorilla_gorilla, but if I use my config file, although it point to same cache directory , but give error message :</div>
<div><br></div><div>perl /nfs/users/nfs_y/yuan/sanger/src/svn/VEP/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i qasim_gtype.vcf -species gorilla -config vep_config_file<br>
2014-06-06 05:57:53 - Read configuration from vep_config_file<br>ERROR: Cache directory /data/blastdb/Ensembl/vep/gorilla/75 not found at /nfs/users/nfs_y/yuan/sanger/src/svn/VEP/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 993.</div>
<div><br></div><div><br></div><div>OK, I think if I delete offline or change species from gorilla to gorilla_gorilla in my config_file, this error has gone, but if I use -vcf I still got error : 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.</div>
<div><br></div><div>if I remove -vcf, it works ok.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">yuan</font></span><div><div class="h5">
<br><div><div>On 5 Jun 2014, at 10:27, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><blockquote type="cite"><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/" target="_blank">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><font color="#888888"><br>
yuan</font></span><br>_______________________________________________<br>
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_______________________________________________<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>
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