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<div class="moz-cite-prefix">Reinstalled VEP and it worked. Thanks
for the quick fix.<br>
<br>
Best,<br>
Sebastian<br>
<br>
Am 09.02.2016 um 12:43 schrieb Will McLaren:<br>
</div>
<blockquote
cite="mid:CAMVEDX3o1XNMPS7QqogFjYFJdd+jwq4SoyZOucc7gADm60vO5Q@mail.gmail.com"
type="cite">
<div dir="ltr">Hi again,
<div><br>
</div>
<div>Thanks for that - it was the JSON output that was the
issue.</div>
<div><br>
</div>
<div>I've patched a fix to ensembl-variation on release/83 - if
you re-run INSTALL.pl or do a git pull in ensembl-variation
(if you used git) you should get the fix.</div>
<div><br>
</div>
<div>Thanks again,</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 9 February 2016 at 11:21, 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">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi,<br>
<br>
I am using json output format. <br>
<br>
The command line is: <br>
<br>
perl /path/to/vep/<a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a> \ <br>
-i /tmp/vep_failed2.vcf \ <br>
-o /tmp/vep_annots.json \ <br>
--offline \ <br>
--cache \ <br>
--dir /path/to/vep/cache \ <br>
--json \ <br>
--force_overwrite \ <br>
--quiet \ <br>
--no_progress \ <br>
--species=homo_sapiens \ <br>
--buffer_size 5000 \ <br>
--fork 2 \ <br>
--regulatory \ <br>
--merged \ <br>
--ccds \ <br>
--uniprot \ <br>
--hgvs \ <br>
--symbol \ <br>
--numbers \ <br>
--domains \ <br>
--canonical \ <br>
--protein \ <br>
--biotype \ <br>
--uniprot \ <br>
--tsl \ <br>
--appris \ <br>
--gene_phenotype \ <br>
--gmaf \ <br>
--maf_1kg \ <br>
--maf_esp \ <br>
--maf_exac \ <br>
--pubmed \ <br>
--variant_class \ <br>
--no_stats \ <br>
--dont_skip \ <br>
--sift b \ <br>
--polyphen b<br>
<br>
Error message is:<span class=""><br>
Can't call method "rank" on an undefined value at
/path/to/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line
1975<br>
<br>
</span> Regards,<br>
Sebastian
<div>
<div class="h5"><br>
<br>
Am 09.02.2016 um 11:34 schrieb Will McLaren:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Sebastian,
<div><br>
</div>
<div>The script shouldn't die in this situation -
which output format are you using? It would be
useful if you could share the exact command you
are using.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 9 February 2016 at
10:22, Sebastian Ginzel <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:sginze2s@inf.h-brs.de"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:sginze2s@inf.h-brs.de">sginze2s@inf.h-brs.de</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<pre style="color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px">Hi Will,
thanks for your explanation.
Do you have any suggestion how to filter these variants before processing?
Because VEP fails and stops annotating the rest of the VCF.
Regards,
Sebastian
> Hi Sebastian,
>
> In some cases when using the RefSeq transcript cache, the mappings we are
> provided by NCBI for a particular transcript may cause issues.
>
> In this case our database contains duplicate entries for NM_001271893.1,
> one of which is marked as a protein coding transcript but has no defined
> CDS. Your variant overlaps this duplicate, and because of the conflicting
> definition the VEP doesn't know what to call the variant and a warning is
> given on STDERR and in the warnings file.
>
> I would consider it safe to filter out or ignore any cases where we are
> unable to assign a consequence type such as this as they typically
> correspond to transcript annotations that are faulty to begin with.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 3 February 2016 at 14:07, Sebastian Ginzel <sginze2s at <a moz-do-not-send="true" href="http://inf.h-brs.de" target="_blank">inf.h-brs.de</a>> wrote:
>
>> Hi Ensembl,
>>
>> I am trying to annotate a variant using VEP v83 with the
>> homo_sapiens_merged cache.
>>
>> When I reach this variant in my VCF file:
>> 2 239832097 . A T 100 PASS . . .
>>
>> VEP fails with:
>> Can't call method "rank" on an undefined value at
>> /path/to/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1975
>>
>> The function vf_to_consequnces returns '?' as a consequence for this
>> variant.
>>
>> I have taken the liberty to attach the Data::Dumper output for a couple of
>> relevant variables as well as the parameters used to call the VEP script.
>>
>> When looking at the result of vf_to_consequences it seems that the Codons
>> and Amino_acids fields are undefined (line 98 & 100), although the variant
>> is predicted protein_coding (line 85).
>>
>> I got the same error for variants up- and downstream of that location.
>>
>> Can anyone confirm this? And if so: has an idea on how to fix it?
>>
>>
>> Best wishes,
>> Sebastian Ginzel
>>
>>
>>
>>
>>
>> _______________________________________________
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>>
>></span></pre>
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