<div dir="ltr">Hi all,<div><br></div><div>This is just a warning, not an error (note it says - "OK!" and "All done").</div><div><br></div><div>The warning should be fixed now if you re-download the ensembl-tools package.</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 22 July 2015 at 19:31, Balanis, Nikolas G. <span dir="ltr"><<a href="mailto:NBalanis@mednet.ucla.edu" target="_blank">NBalanis@mednet.ucla.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">Hello Cyriac and other members,<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">So there was a mistake in what I emailed, It’s not in fact what I ran.
<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">I did run it with the <a href="http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_" target="_blank">ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_</a>81_GRCh{37,38}.tar.gz
$VEP_DATA instructions. In fact the error message references version 80. <u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">which is the previous version I had installed and used successfully. I have been trying to install version 81 just because I wanted to update to the newest version.
<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">Here is my .vep folder
<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">~/.vep$ ls<br>
homo_sapiens homo_sapiens_vep_81_GRCh37.tar.gz homo_sapiens_vep_81_GRCh38.tar.gz<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">cd homo_sapiens<br>
<a href="mailto:niko@niko-VirtualBox:~/.vep/homo_sapiens$" target="_blank">niko@niko-VirtualBox:~/.vep/homo_sapiens$</a> ls<br>
81_GRCh37 81_GRCh38<br>
<a href="mailto:niko@niko-VirtualBox:~/.vep/homo_sapiens$" target="_blank">niko@niko-VirtualBox:~/.vep/homo_sapiens$</a>
<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black"> <u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">Is there something else I am missing? It seems to me the error is only on version 38. In fact when i run these commands to update GRCh37 I still get the error about
38. If there any other information that would be useful?<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">niko@niko-VirtualBox:~/vep$ perl INSTALL.pl --AUTO a --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA<br>
Using non-default installation directory /home/niko/vep - you will probably need to add /home/niko/vep to your PERL5LIB<br>
<br>
Setting up directories<br>
<br>
Downloading required files<br>
- fetching ensembl<br>
** GET <a href="https://github.com/Ensembl/ensembl/archive/release/81.zip" target="_blank">https://github.com/Ensembl/ensembl/archive/release/81.zip</a> ==> 302 Found (1s)<br>
** GET <a href="https://codeload.github.com/Ensembl/ensembl/zip/release/81" target="_blank">https://codeload.github.com/Ensembl/ensembl/zip/release/81</a> ==> 200 OK (42s)<br>
- unpacking /home/niko/vep/Bio/tmp/ensembl.zip<br>
- moving files<br>
- fetching ensembl-variation<br>
** GET <a href="https://github.com/Ensembl/ensembl-variation/archive/release/81.zip" target="_blank">
https://github.com/Ensembl/ensembl-variation/archive/release/81.zip</a> ==> 302 Found (1s)<br>
** GET <a href="https://codeload.github.com/Ensembl/ensembl-variation/zip/release/81" target="_blank">
https://codeload.github.com/Ensembl/ensembl-variation/zip/release/81</a> ==> 200 OK (5s)<br>
- unpacking /home/niko/vep/Bio/tmp/ensembl-variation.zip<br>
- moving files<br>
- fetching ensembl-funcgen<br>
** GET <a href="https://github.com/Ensembl/ensembl-funcgen/archive/release/81.zip" target="_blank">
https://github.com/Ensembl/ensembl-funcgen/archive/release/81.zip</a> ==> 302 Found<br>
** GET <a href="https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/81" target="_blank">
https://codeload.github.com/Ensembl/ensembl-funcgen/zip/release/81</a> ==> 200 OK (2s)<br>
- unpacking /home/niko/vep/Bio/tmp/ensembl-funcgen.zip<br>
- moving files<br>
- fetching BioPerl<br>
** GET <a href="https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip" target="_blank">
https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip</a> ==> 302 Found<br>
** GET <a href="https://codeload.github.com/bioperl/bioperl-live/zip/release-1-6-924" target="_blank">
https://codeload.github.com/bioperl/bioperl-live/zip/release-1-6-924</a> ==> 200 OK (2s)<br>
- unpacking /home/niko/vep/Bio/tmp/release-1-6-924.zip<br>
- moving files<br>
<br>
Testing VEP script<br>
./t/filter_vep.t ................ ok <br>
./t/convert_cache.t ............. ok <br>
./t/variant_effect_predictor.t .. 81/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 88/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 89/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 90/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 91/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 92/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 93/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. 94/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
For homo_sapiens_otherfeatures_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br>
./t/variant_effect_predictor.t .. 95/? For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<span class=""><br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.<br></span>
./t/variant_effect_predictor.t .. ok <br>
All tests successful.<br>
Files=3, Tests=126, 540 wallclock secs ( 0.02 usr 0.03 sys + 20.52 cusr 4.91 csys = 25.48 CPU)<br>
Result: PASS<br>
- OK!<br>
<br>
All done<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">I get the same error If I try installing version 38. Im not sure why it errors out in that case either as wouldn't I be updating the database to version 81.<br>
My wild guess is this has something to do with the fasta version 81 of grch38? Any clues? Is there any other information that would be useful?
<u></u><u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">Thank you so much for your help.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">-Nikolas Balanis<u></u><u></u></span></p><span class="">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">Also note that these instructions are just for installing VEP locally to run offline. You won't install all of Ensembl's API and tools.<u></u><u></u></span></p>
</span><p><span style="font-size:10.0pt;line-height:120%;font-family:"Tahoma",sans-serif;color:black">yes for now I am only using vep. -niko<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Nikolas,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">The only fix in those commands is to download the v81 cache instead of v79. See the highlighted fix below...<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">rsync -zvh rsync://<a href="http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_" target="_blank">ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_</a><b><span style="background:#f9cb9c">81</span></b>_GRCh{37,38}.tar.gz
$VEP_DATA</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Also note that these instructions are just for installing VEP locally to run offline. You won't install all of Ensembl's API and tools.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">~Cyriac<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Mon, Jul 20, 2015 at 9:58 PM, Balanis, Nikolas G. <<a href="mailto:NBalanis@mednet.ucla.edu" target="_blank">NBalanis@mednet.ucla.edu</a>> wrote:<u></u><u></u></p>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">Hello I am looking for the solution to this problem.
<i>I googled and looked on throught the archives but I am not sure how to fix this.
</i>I am installing vep based on the instructions from <a href="https://github.com/ckandoth/vcf2maf" target="_blank">
https://github.com/ckandoth/vcf2maf</a><u></u><u></u></span></p>
<pre><code><span style="color:black">export VEP_PATH=~/vep<u></u><u></u></span></code></pre>
<pre><code><span style="color:black">export VEP_DATA=~/.vep</span></code><span style="color:black"><u></u><u></u></span></pre>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><u></u> <u></u></span></p>
<pre><code><span style="color:black">mkdir $VEP_PATH; cd $VEP_PATH<u></u><u></u></span></code></pre>
<pre><code><span style="color:black">curl -LO <a href="https://github.com/Ensembl/ensembl-tools/archive/release/81.tar.gz" target="_blank">https://github.com/Ensembl/ensembl-tools/archive/release/81.tar.gz</a><u></u><u></u></span></code></pre>
<pre><code><span style="color:black">tar -zxf 81.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'</span></code><span style="color:black"><br><br><code>rsync -zvh rsync://<a href="http://ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh%7B37,38%7D.tar.gz" target="_blank">ftp.ensembl.org/ensembl/pub/release-81/variation/VEP/homo_sapiens_vep_79_GRCh{37,38}.tar.gz</a> $VEP_DATA<u></u><u></u></code></span></pre>
<pre><code><span style="color:black">cat $VEP_DATA/*.tar.gz | tar -izxf - -C $VEP_DATA</span></code><span style="color:black"><br><br><br><code>cd $VEP_PATH<u></u><u></u></code></span></pre>
<pre><code><span style="color:black">perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA<u></u><u></u></span></code></pre>
<pre><code><span style="color:black">perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh38 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA<u></u><u></u></span></code></pre>
<pre><span style="color:black"><br><br><code>I get this warning message below when I perform either of the last 2 instructions. I can't</code><br><code>seem to figure this out. Everything should be release 81 so I am quite confused. </code><br><code>What are the steps to fix this?</code><u></u><u></u></span></pre>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">For homo_sapiens_core_80_38 there is a difference in the software release (81) and the database release (80). You should update one
of these to ensure that your script does not crash.<br>
For homo_sapiens_variation_80_38 there is a difference in the software release (81) and the database release (80). You should update one of these to ensure that your script does not crash.</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><u></u><u></u></span></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div class="MsoNormal" align="center" style="text-align:center">
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