[ensembl-dev] VEP 79 API problems

[Will McLaren]

Hi again,

I can't recreate the problem with that input file I'm afraid, either on my
normal setup or scrubbing PERL5LIB and starting from scratch.

See commands I used and input below.

Perhaps you haven't got release/79 of ensembl-tools too?

Have you tried running the installer from within
ensembl-tools/scripts/variant_effect_predictor? This shouldn't affect your
PERL5LIB or other git checkouts.

Will

===================

mkdir ~/src/tmp
cd ~/src/tmp
git clone --branch release/79 https://github.com/Ensembl/ensembl-tools.git
git clone --branch release/79 https://github.com/Ensembl/ensembl.git
git clone --branch release/79
https://github.com/Ensembl/ensembl-variation.git
git clone --branch release/79 https://github.com/Ensembl/ensembl-funcgen.git
export
PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/
perl ensembl-tools/scripts/variant_effect_predictor/
variant_effect_predictor.pl  -i ~/Downloads/input.vcf  -database
2015-06-03 17:09:54 - Starting...
2015-06-03 17:09:54 - Detected format of input file as vcf
2015-06-03 17:09:54 - Read 1 variants into buffer
2015-06-03 17:09:54 - Reading transcript data from cache and/or database
[================================================================================================================================]
 [ 100% ]
2015-06-03 17:10:00 - Retrieved 7 transcripts (0 mem, 0 cached, 7 DB, 0
duplicates)
2015-06-03 17:10:00 - Analyzing chromosome 1
2015-06-03 17:10:00 - Analyzing variants
[================================================================================================================================]
 [ 100% ]
2015-06-03 17:10:00 - Calculating consequences
2015-06-03 17:10:00 - Processed 1 total variants (0 vars/sec, 0 vars/sec
total)
2015-06-03 17:10:00 - Wrote stats summary to
variant_effect_output.txt_summary.html
2015-06-03 17:10:00 - Finished!




On 3 June 2015 at 16:51, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hi Will,
>
> I've been checking and I can't see any unintended whitespace or problem
> with tabulations.
> I've no issues with old vep 75 script and API. I've updated the Bioperl
> lib in $PERL5LIB variable from 1.2.3 to 1.6.1 (I didn't see this change
> before sorry) however I'm still getting all those errors.
>
> Here's a link where you can download the VCF I'm using as input:
> https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0
>
> Thank you.
>
> Best regards,
> Guille.
>
>
> On 03/06/15 17:30, Will McLaren wrote:
>
> Hi Guille,
>
> It looks to me like your input is not being parsed properly.
>
>  Check the formatting of your input VCF; double check that it is valid
> VCF, and that you haven't got any unintended whitespace on any of the lines.
>
>  If you still have an issue, can you send a line or two of the input that
> recreates these issues?
>
>  Thanks
>
>  Will McLaren
> Ensembl Variation
>
>
> On 3 June 2015 at 16:16, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>>  Dear devs,
>>
>> I'm trying ensembl 79 VEP.
>>
>> This is my dummy input VCF: http://pastebin.com/kFKWH50q#
>>
>> I've cloned and installed API from github as always (this step is
>> repeated for variaton, funcgen and compara):
>>
>>    - git clone --branch release/79 https://github.com/Ensembl/ensembl.git
>>    ensembl_79
>>
>> PERL5LIB env variable is correctly pointing to the cloned API:
>>
>>    - echo $PERL5LIB
>>
>>    /share/apps/local/bioperl-live:/share/apps/src/ensembl_79/modules:/share/apps/src/ensembl_79-compara/modules:/share/apps/src/ensembl_79-variation/modules:/share/apps/src/ensembl_79-functgenomics/modules
>>
>> However I'm getting a lot of errors I really don't understand. It seems
>> like a bug with API installation with me. If I change $PERL5LIB variable to
>> point to 75 API (previous version I was using) I can't reproduce the errors
>> VEP script works for this old 75 version.
>>
>> I've been reading the docs again and I can't seen any additional PERL
>> library requirement.
>>
>> Here's the error log: http://pastebin.com/VvQrkEQZ
>>
>>
>> Thank you!
>>
>> Best regards,
>> Guille.
>>
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>>
>
>
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