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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Anja,
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<div>Please see below my responses to your queries in bold. Hope that helps.</div>
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<div>Thanks</div>
<div>Abhishek<br>
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<div id="divRpF129553" 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 3:53 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 class="">Thank you for the extra details.</div>
<div class=""><br class="">
</div>
<div class="">Could you please confirm one more time the return value for running:</div>
<div class=""><br class="">
</div>
<div class="">tabix -fh <span class="" style="font-family:Arial; font-size:small">/home/VEP/Plugins/dbNSFP4.0b2a.txt.gz</span> 1:1-1 2>&1</div>
<div class=""><br class="">
</div>
<div class="">It should be #chr    pos(1-based)    ref     alt     aaref   aaalt   rs_dbSNP151     hg19_chr ….</div>
<div class=""><br class="">
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<div class=""><b>I get exactly the same output as you mentioned, on running the tabix -fh command</b></div>
<div class=""><br>
</div>
<div class="">The error (ERROR: Could not read headers from dbNSFP4.0b2a.txt.gz) most likely points to a missing header line in the dbNSFP file.</div>
<div class=""><br class="">
</div>
<div class="">If the plugin couldn't read from the dbNSFP file the error would be <i class="">ERROR: Data file dbNSFP4.0b2a.txt.gz not found</i></div>
<div class=""><br class="">
</div>
<div class="">There are 2 things which slightly confuse me:</div>
<div class=""><br class="">
</div>
<div class="">1) If you run vep with /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</div>
<div class="">ALL --tab --force_overwrite --port 3337</div>
<div class="">I would expect the full path name in the error message: ERROR: Could not read headers from /home/VEP/Plugins/dbNSFP4.0b2a.txt.gz</div>
<div class=""><br>
</div>
<div class=""><b>Yes, true, I do get the full path name in the error message</b></div>
<div class=""><br class="">
</div>
<div class="">2) tabix -H is not supported by tabix version: 0.2.5. But you are able to run tabix -H?</div>
<div class=""><br class="">
</div>
<div class=""><b>When I just run tabix (version 0.2.5) from my command line, the list of available options shows that the -H option for printing just the header line is available.</b></div>
<div class=""><br class="">
</div>
<div class="">Once we figured out what is going on you need to switch to a more recent <a href="https://github.com/Ensembl/VEP_plugins/blob/release/97/dbNSFP.pm" class="" target="_blank">release version for the plugin</a>. In the more recent versions of the
 dbNSFP plugin we are dealing with the different header names for grch37 and grch38 coordinates that have been introduced by dbNSFP for their last file version 2.*, 3.* and 4.*. But this is only relevant after the plugin has retrieved the header line.</div>
<div class=""><br class="">
</div>
<div class="">Thank you,</div>
<div class="">Anja</div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 3 Jun 2019, at 14:43, 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">
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<font face="Arial" size="3" class="">Dear Anja,</font>
<div class=""><font face="Arial" size="3" class=""><br class="">
</font></div>
<div class=""><font face="Arial" size="3" class="">Thanks for your response.</font></div>
<div class=""><font face="Arial" size="3" class=""><br class="">
</font></div>
<div class=""><font face="Arial" size="3" class="">I'm using the VEP version 93 and perl version v5.16.3</font></div>
<div class=""><font face="Arial" size="3" class=""><br class="">
</font></div>
<div class=""><font face="Arial" size="3" class="">Thanks</font></div>
<div class=""><font face="Arial" class=""><font size="3" class="">Abhishek</font><br class="">
</font>
<div class="" style="font-family:"Times New Roman"; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF20960" 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>Monday, June 03, 2019 2:25 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="">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 class=""><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="">
<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">
<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=""><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=""><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=""><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>
</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>
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