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<p>Hi Hans,</p>
<p>Have you forgotten to include --offline when using new VEP? This
will trigger the use of cache files.<br>
</p>
Best wishes,<br>
<br>
Sarah<br>
<div class="moz-cite-prefix"><br>
On 28/03/2017 22:34, Hans Vasquez-Gross wrote:<br>
</div>
<blockquote
cite="mid:CAPvh4w3=dWRg2xEhadYm9ec9jPdod6Sjp_uDWnJUkdOrjP4c8w@mail.gmail.com"
type="cite">
<div dir="ltr">Hi ENSEMBL,<br clear="all">
<div><br>
</div>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div style="font-size:12.8px">I have successfully
been using ensembl tool release 75 for a while.
Now, I'm planning to start using the github
version because of the speed increase as well as
new features.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">However, I am having
trouble running VEP. I get the following error.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">
<div><br>
</div>
<div>ernie-sears:ensembl-vep_git_<wbr>beta
havasquezgross$ ./<a moz-do-not-send="true"
href="http://vep.pl/" target="_blank">vep.pl</a> --species
triticum_aestivum -i Josh_mut_v4.mapspart2.<wbr>HetMinCov3HetMinPer15HomMinCov<wbr>2.vcf
-o Josh_mut_v4.mapspart2.<wbr>HetMinCov3HetMinPer15HomMinCov<wbr>2.vep.vcf
--fork 4 --db_version 34 --assembly TGACv1
--force_overwrite</div>
<div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 1</div>
<div><br>
</div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 2</div>
<div><br>
</div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 3</div>
<div><br>
</div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 4</div>
<div><br>
</div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 5</div>
<div><br>
</div>
<div>WARNING: Chromosome
TGACv1_scaffold_001462_1AL not found in
annotation sources or synonyms on line 6</div>
<div><br>
</div>
<div><br>
</div>
<div>However, looking at the VEP cache, this
folder is actually present. Do you have any
suggestions why this error could be showing
up?</div>
<div><br>
</div>
<div>
<div>ernie-sears:TGACv1_scaffold_<wbr>001462_1AL
havasquezgross$ pwd</div>
<div>/Users/havasquezgross/.vep/<wbr>triticum_aestivum/34_TGACv1/<wbr>TGACv1_scaffold_001462_1AL</div>
<div>ernie-sears:TGACv1_scaffold_<wbr>001462_1AL
havasquezgross$ ls -1</div>
<div>1-1000000.gz</div>
<div>1-1000000_var.gz</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>I also have a symlink in the
.vep/triticum_aestivum folder which points the
directory 34_TGACv1 to 34 as well, so I can
run with the old release 75 version which I
have been using for years. Running with
release 75 doesn't print this same warning and
produces results.</div>
<div><br>
</div>
<div>time ./<a moz-do-not-send="true"
href="http://variant_effect_predictor.pl/"
target="_blank">variant_effect_predictor.pl</a> -species
triticum_aestivum -i v41.mapspart2.<wbr>HetMinCov3HetMinPer15HomMinCov<wbr>2.vcf
-o v41.mapspart2.<wbr>HetMinCov3HetMinPer15HomMinCov<wbr>2.vep.vcf
--fork 4 --offline --db_version 34
--force_overwrite --compress gzcat --vcf<br>
</div>
<div>[...clip...]</div>
<div>
<div>2017-03-27 15:22:32 - Writing output</div>
<div>2017-03-27 15:22:32 - Processed 239683
total variants (585 vars/sec, 781 vars/sec
total)</div>
<div>2017-03-27 15:22:34 - Wrote stats summary
to v41.mapspart2.<wbr>HetMinCov3HetMinPer15HomMinCov<wbr>2.vep.vcf_summary.html</div>
<div>2017-03-27 15:22:34 - Finished!</div>
<div><br>
</div>
<div>real<span class="gmail-m_-8807591114552963403gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>5m9.791s</div>
<div>user<span class="gmail-m_-8807591114552963403gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>17m47.120s</div>
<div>sys<span class="gmail-m_-8807591114552963403gmail-Apple-tab-span" style="white-space:pre-wrap"> </span>5m17.075s</div>
</div>
<div><br>
</div>
<div>Thank you,</div>
<div>-Hans</div>
</div>
</div>
</div>
</div>
</div>
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</blockquote>
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