<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body class="" style="word-wrap:break-word; line-break:after-white-space" fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">
<div style="direction: ltr; color: rgb(0, 0, 0);"><font size="2" face="Arial">Dear Anja,
</font>
<div><font size="2" face="Arial"><br>
</font></div>
<div><font size="2" face="Arial">Thanks for responding to my email. </font></div>
<div><font size="2" face="Arial"><br>
</font></div>
<div><font size="2" face="Arial">The header line that is returned on running tabix -H seems fine. </font></div>
<div><font size="2" face="Arial"><br>
</font></div>
<div><font size="2" face="Arial">Here is the VEP command that I'm running:</font></div>
<div><font size="2" face="Arial"><br>
</font></div>
<div>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures"><font size="2" face="Arial">/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 style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures"><font size="2" face="Arial"><br>
</font></span></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures"><font size="2" face="Arial">The </font></span><span style="font-family: Arial; font-size: small;">/home/VEP/ path contains the Plugins subdirectory (which contains the </span><span style="font-family: Arial; font-size: small;">dbNSFP4.0b2a.txt.gz
 file) as well as the cache folder homo_sapiens.</span></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-family: Arial; font-size: small;"><br>
</span></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-family: Arial; font-size: small;">Thanks for your help!</span></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-family: Arial; font-size: small;"><br>
</span></p>
<p style="margin-right: 0px; margin-left: 0px; font-stretch: normal; line-height: normal;">
<span style="font-family: Arial; font-size: small;">Abhishek</span></p>
</div>
<div style="font-family: Tahoma; font-size: 10pt;"><br>
<div style="font-family:Times New Roman; color:#000000; font-size:16px">
<hr tabindex="-1">
<div id="divRpF243944" 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> Thursday, May 23, 2019 3:52 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP dbNSFP error<br>
</font><br>
</div>
<div></div>
<div>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><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>
</div>
<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>
</div>
<span class="" style="font-family:Helvetica; font-size:12px; 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; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; 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">
<span class="" style="font-family:Helvetica; font-size:12px; 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; float:none; display:inline!important">Dev
 mailing list    </span><a href="mailto:Dev@ensembl.org" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px" target="_blank">Dev@ensembl.org</a><br class="" style="font-family:Helvetica; font-size:12px; 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">
<span class="" style="font-family:Helvetica; font-size:12px; 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; float:none; display:inline!important">Posting
 guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span></span><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br class="" style="font-family:Helvetica; font-size:12px; 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">
<span class="" style="font-family:Helvetica; font-size:12px; 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; float:none; display:inline!important">Ensembl
 Blog:<span class="Apple-converted-space"> </span></span><a href="http://www.ensembl.info/" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px" target="_blank">http://www.ensembl.info/</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>