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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font face="Arial" size="3">Dear Anja,</font>
<div><font face="Arial" size="3"><br>
</font></div>
<div><font face="Arial" size="3">Thanks for your response.</font></div>
<div><font face="Arial" size="3"><br>
</font></div>
<div><font face="Arial" size="3">I'm using the VEP version 93 and perl version v5.16.3</font></div>
<div><font face="Arial" size="3"><br>
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<div><font face="Arial" size="3">Thanks</font></div>
<div><font face="Arial"><font size="3">Abhishek</font><br>
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<div id="divRpF20960" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Dev [dev-bounces@ensembl.org] on behalf of Anja Thormann [anja@ebi.ac.uk]<br>
<b>Sent:</b> Monday, June 03, 2019 2:25 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP dbNSFP error<br>
</font><br>
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<div>Dear Abhishek,
<div class=""><br class="">
</div>
<div class="">so far I wasn’t able to reproduce the error. I have been running tests with the same dbNSFP file and tabix version. Could you please also let me know your perl version and your vep version?</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Anja</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 26 May 2019, at 15:47, Abhishek Nag <<a href="mailto:abhishek@well.ox.ac.uk" class="" target="_blank">abhishek@well.ox.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<div class="" style="direction:ltr"><font size="2" face="Arial" class="">Dear Anja,</font>
<div class=""><font size="2" face="Arial" class=""><br class="">
</font></div>
<div class=""><font size="2" face="Arial" class="">Thanks for responding to my email. </font></div>
<div class=""><font size="2" face="Arial" class=""><br class="">
</font></div>
<div class=""><font size="2" face="Arial" class="">The header line that is returned on running tabix -H seems fine. </font></div>
<div class=""><font size="2" face="Arial" class=""><br class="">
</font></div>
<div class=""><font size="2" face="Arial" class="">Here is the VEP command that I'm running:</font></div>
<div class=""><font size="2" face="Arial" class=""><br class="">
</font></div>
<div class="">
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style=""><font size="2" face="Arial" class="">/apps/well/ensembl-tools/93/ensembl-vep/vep -i variants.txt -o output.txt --cache --dir /home/VEP/ --plugin dbNSFP,/home/VEP/Plugins/dbNSFP4.0b2a.txt.gz,ALL
--tab --force_overwrite --port 3337</font></span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style=""><font size="2" face="Arial" class=""><br class="">
</font></span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style=""><font size="2" face="Arial" class="">The </font></span><span class="" style="font-family:Arial; font-size:small">/home/VEP/ path contains the Plugins subdirectory
(which contains the </span><span class="" style="font-family:Arial; font-size:small">dbNSFP4.0b2a.txt.gz file) as well as the cache folder homo_sapiens.</span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style="font-family:Arial; font-size:small"><br class="">
</span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style="font-family:Arial; font-size:small">Thanks for your help!</span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style="font-family:Arial; font-size:small"><br class="">
</span></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><span class="" style="font-family:Arial; font-size:small">Abhishek</span></p>
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<div id="divRpF243944" class="" style="direction:ltr"><font face="Tahoma" size="2" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Dev [<a href="mailto:dev-bounces@ensembl.org" class="" target="_blank">dev-bounces@ensembl.org</a>]
on behalf of Anja Thormann [<a href="mailto:anja@ebi.ac.uk" class="" target="_blank">anja@ebi.ac.uk</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 23, 2019 3:52 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Ensembl developers list<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] VEP dbNSFP error<br class="">
</font><br class="">
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<div class=""></div>
<div class="">Dear Abhishek,
<div class=""><br class="">
</div>
<div class="">could you please run tabix -H dbNSFP4.0b2a.txt.gz and let me know if it returns the header line starting with #chr pos(1-based)..? If that is the case could you please let me know who exactly your are running the VEP command together with the
dbNSFP plugin command? If the header is returned correctly I’m wondering if the dbNSFP file path is maybe not found correctly by the plugin.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Anja<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 23 May 2019, at 13:53, Abhishek Nag <<a href="mailto:abhishek@well.ox.ac.uk" class="" target="_blank">abhishek@well.ox.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<font face="Arial" size="2" class="">Hi,</font>
<div class=""><font face="Arial" size="2" class=""><br class="">
</font></div>
<div class=""><font face="Arial" size="2" class="">I have been trying to use the dbNSFP database to annotate my variants. Currently, I'm trying to use the latest version of the database (v4.0), but I have also tried using the version 3.5. With both versions,
I'm getting the following error message whenever I'm trying to run it -</font></div>
<div class=""><font face="Arial" size="2" class=""><br class="">
</font></div>
<div class="">
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class=""><b class="">Failed to instantiate plugin dbNSFP: ERROR: Could not read headers from dbNSFP4.0b2a.txt.gz</b></font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class=""><br class="">
</font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class="">When I zcat the database file, I am able to read the header line, which was obtained from one of the chromosome files, as suggested in the online
manual.</font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class=""><br class="">
</font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class="">The formatting steps for the database (including tab indexing) seem to have gone fine, so I'm not sure where the problem is. Also, I am being able
to use the other VEP Plugins just fine; for now, I'm getting this error messge with only the dbNSFP plugin.</font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class=""><br class="">
</font></p>
<p class="" style="margin-right:0px; margin-left:0px; line-height:normal"><font face="Arial" size="2" class="">It would be great if I could have some pointers regarding where the issue might be. </font></p>
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<div class=""><font face="Arial" size="2" class=""><br class="">
</font></div>
<div class=""><font face="Arial" size="2" class="">Many Thanks</font></div>
<div class=""><font face="Arial" size="2" class="">Abhishek</font></div>
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