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<div class="moz-cite-prefix">Hi Will,<br>
<br>
the --write-cache option was enabled, I don't remember why or who
enabled it. I think I can safely remove it from my command line,
but I guess I should re-download the cache?<br>
<br>
Regards,<br>
Sebastian Ginzel<br>
<br>
On 01.10.2015 17:07, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0W1Kgm=17ZNoZsPHML8rOb=50tCckACBzh4=9APuUE=Q@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Sebastian,
<div><br>
</div>
<div>Can you share your full command line?</div>
<div><br>
</div>
<div>That line of code should not be triggered unless you have
either --database (which should cause the script to fail on
startup) or --write_cache (which you shouldn't use unless you
really know what you're doing!) enabled.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 1 October 2015 at 14:16, Sebastian
Ginzel <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:sginze2s@inf.h-brs.de" target="_blank">sginze2s@inf.h-brs.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I am using VEP 80 and use the --offline and --cache option,
which usually works fine, but now fails on one input file
with the message:<br>
<br>
Can't call method "db" on an undefined value at
/path_to_lib/ensembl_80/lib/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 6360, <GEN0> line 190004<br>
<br>
After digging into the code I found that this line is called
when a variant is not available in the cache and VEP tries
to retrieve the information from the database via through
the get_variations_from_region function.<br>
<br>
The line where the script fails is:<br>
if(defined($config->{vfa}->db)) {<br>
<br>
Other functions such as 'have_pubmed' have an additional
condition which prevents the error:<br>
if(defined($config->{vfa}) &&
defined($config->{vfa}->db)) {<br>
<br>
I fixed the error for my VEP script by adding the
"defined($config->{vfa})" condition. But now I am
wondering if the error is intentional and if not which
should be the default return value, if the script is running
in offline mode.<br>
<br>
<br>
Best wishes,<br>
Sebastian Ginzel<br>
<br>
<br>
<br>
<br>
<br>
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