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Sorry I misswrote, when using 1) I get no warnings, when I use cache
2) I get the warnings.<br>
<br>
<div class="moz-cite-prefix">On 07/07/15 13:53, Guillermo Marco
Puche wrote:<br>
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<blockquote cite="mid:559BBDCA.9080002@sistemasgenomicos.com"
type="cite">
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Hello,<br>
<br>
After a few weeks off and re-testing all the possible workarounds
I can conclude that "indexing" VEP cache with convert_cache.pl
script brakes it.<br>
I've now two versions of VEP 80 cache, 1) out of the box (non
indexed) 2) indexed with convert_cache.pl<br>
When I use 1) I get all the warnings, when I use version 2)
performance is much better but I get tons and tons of warnings
like those posted in previous mails.<br>
<br>
I've tried indexing with tabix 0.2.5 and 0.2.6 and I get same
warnings. So I don't think tabix version is the problem.<br>
I hadn't this issue when I was using convert_cache.pl from version
75 build. Any ideas what could have changed in this script to
cause this behavior? Indexing cache with convert_cache.pl finishes
correctly without any warning or error.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/06/15 15:43, Guillermo Marco
Puche wrote:<br>
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<blockquote cite="mid:557AE205.3060203@sistemasgenomicos.com"
type="cite">
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Hi Nicolas,<br>
<br>
Locale is exactly the same on both machines.<br>
<br>
LANG=en_US.UTF-8<br>
LANGUAGE=en_US<br>
LC_CTYPE="en_US.UTF-8"<br>
LC_NUMERIC=es_ES.UTF-8<br>
LC_TIME=es_ES.UTF-8<br>
LC_COLLATE="en_US.UTF-8"<br>
LC_MONETARY=es_ES.UTF-8<br>
LC_MESSAGES="en_US.UTF-8"<br>
LC_PAPER=es_ES.UTF-8<br>
LC_NAME=es_ES.UTF-8<br>
LC_ADDRESS=es_ES.UTF-8<br>
LC_TELEPHONE=es_ES.UTF-8<br>
LC_MEASUREMENT=es_ES.UTF-8<br>
LC_IDENTIFICATION=es_ES.UTF-8<br>
LC_ALL=<br>
<br>
Tried export LC_ALL=C and I still got warnings on machine2.
Anyways, thank you for your help.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 12/06/15 15:36, Nicolas
Thierry-Mieg wrote:<br>
</div>
<blockquote cite="mid:557AE06F.5000101@imag.fr" type="cite">On
06/12/2015 03:21 PM, Guillermo Marco Puche wrote: <br>
<blockquote type="cite">Hi Will, <br>
<br>
This is the command: <br>
<br>
* variant_effect_predictor.pl -i example_GRCh38.vcf -o <br>
annotation_example_GRCh38.vcf -database -hgvs -cache
-dir_cache <br>
/home/gmarco/ensembl_80/cache <br>
<br>
I've tried on another machine (machine2) and I dont' get the
error. <br>
Gonna try to re-install the exact same version of Perl on
both machines. <br>
If this continues failing then I've no idea what's going on.
<br>
Tried both version of bioperl 1.2.3 and 1.6.1 on both
machines and both <br>
work good on machine2 and show warnings on machine1. <br>
Tried both versions of tabix 0.2.5 and 0.2.6 on both
machines and both <br>
work good on machine2 and show warnings on machine1. <br>
<br>
* Machine1 Warnings: <br>
This is perl 5, version 14, subversion 4 (v5.14.4) built
for <br>
x86_64-linux <br>
<br>
* Machine2 NO warnings: <br>
This is perl 5, version 18, subversion 2 (v5.18.2) built
for <br>
x86_64-linux-gnu-thread-multi (with 41 registered
patches, see perl <br>
-V for more detail) <br>
<br>
Maybe it's not a perl issue. Then I've no clue what could be
causing the <br>
issue. <br>
</blockquote>
<br>
what does "locale" say on the two machines? I've had strange
bugs before that were caused by locale settings, as for
example GNU "sort" behaves differently depending on that! <br>
No idea if this could come into play with VEP, but try export
LC_ALL=C before running the command. <br>
<br>
<br>
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<br>
<br>
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<br>
<div class="moz-signature">-- <br>
<title>Guillermo Marco Puche - Firma</title>
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<p><span style="font-size:12px;"><span
style="font-family:arial,helvetica,sans-serif;"><span
style="color:#000066;"><strong>Guillermo Marco
Puche</strong><br>
<br>
Bioinformatician, Computer Science Engineer<br>
Sistemas Genómicos S.L.<br>
Phone: +34 902 364 669 (Ext.777)<br>
Fax: +34 902 364 670</span><br>
<a href="www.sistemasgenomicos.com" target="_blank"><span
style="color:#000066;">www.sistemasgenomicos.com</span></a></span></span></p>
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