<div dir="ltr">Hi Sid,<div><br></div><div>I suspect there is a problem with your cache, perhaps it did not extract correctly.</div><div><br></div><div style>You should have a file named "info.txt" in your [cache_dir]/homo_sapiens/71/ , where [cache_dir] is wherever your cache was installed, typically $HOME/.vep/ .</div>
<div style><br></div><div style>The file looks like this for release 71:</div><div style><br></div><div style><div># CACHE UPDATED 2013-04-02 22:03:30</div><div>host    ens-staging</div><div>port    3306</div><div>user    ensro</div>
<div>build   all</div><div>regulatory      1</div><div>sift    b</div><div>polyphen        b</div><div>cell_types      HeLa-S3,GM06990,U2OS,CD4,IMR90,HL-60,HepG2,Lymphoblastoid,CD133,CD36,K562,GM12878,HUVEC,NHEK,H1ESC,MultiCell,K562b,NH-A,HSMM,HMEC,A549,AG04449,AG04450,AG09309,AG09319,AG10803,Caco-2,Chorion,CMK,GM10847,GM12801,GM12864,GM12865,GM12872,GM12873,GM12874,GM12875,GM12891,GM12892,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,H7ESC,H9ESC,HAEpiC,HCF,HCM,HCPEpiC,HCT116,HEEpiC,HEK293b,HEK293,HepG2b,HGF,HIPEpiC,HNPCEpiC,HRCEpiC,HRE,HRPEpiC,Jurkat,LHSR,MCF7,Medullo,Melano,NB4,NHBE,NHDF-neo,NHLF,NT2-D1,Panc1,PanIslets,PFSK1,SAEC,SKMC,SKNMC,SKNSHRA,Th1,Th2,WERIRB1,RPTEC,ProgFib,HSMMtube,Osteobl,MCF10A-Er-Src,HPAEpiC,Fibrobl,GM12878-XiMat,BJ</div>
<div>sift_version    sift5.0.2</div><div>polyphen_version        2.2.2</div><div>variation_cols  variation_name,failed,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,AFR,AMR,ASN,EUR</div><div><br></div>
<div style>You could also check that it is working using --database in place of --cache (but only to get the cell_type list!!!).</div><div style><br></div><div style>Regards</div><div style><br></div><div style>Will</div>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 14 May 2013 14:58, Siddharth Sethi <span dir="ltr"><<a href="mailto:s.sethi@har.mrc.ac.uk" target="_blank">s.sethi@har.mrc.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 class="HOEnZb"><div class="h5">




<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Hi,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am trying to get the available cell types for Humans, but VEP is not printing the cell types when used –cell_type list</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">ERROR: cell type list not recognised; available cell types are:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">This is command :</p>
<p class="MsoNormal">perl EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --cache -species homo_sapiens --regulatory -cell_type list</p>

<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Also,  it prints : Database will be accessed when using --regulatory; consider using the complete cache containing regulatory data.</p>
<p class="MsoNormal">Can you please tell me what is the complete cache. I downloaded the cache files using the installer , so it should not access the database for regulatory.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thank you.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Regards,</p>
<p class="MsoNormal">Sid</p>
<p class="MsoNormal"> </p>
</div>
<br>
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