[ensembl-dev] VEP 79 API problems

Thu Jun 4 12:12:12 BST 2015

Hi again

If the script is not detecting the input format then it is almost certainly
an issue with the input file. There's very little code that gets run to
detect the format, and it's all internal to the VEP code.

You could write a short script to test the method, just import
detect_format from Bio:EnsEMBL::Variation::Utils::VEP

Does it detect the example_GRCh37.vcf format correctly?

The file you shared on Dropbox works fine for me on my Mac and a Linux box.

Will
On 4 Jun 2015 10:44, "Guillermo Marco Puche" <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hi again Will,
>
> I'm trying with latest ensembl 80.
> If I don't specify *-format vcf* I get the following error:
>
> perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl -i input.vcf -database --force_overwrite
> 2015-06-04 11:36:59 - Starting...
> ERROR: Could not detect input file format
>
>
> If I force format with* -format vcf *I get all the errors. (see error log
> attached). I'm using the same input.vcf file I posted yesterday.
> Just to discard it's not VCF, I've installed a fresh linux on virtual
> machine and just cloned and setup Ensembl and Bioperl. On fresh Linux
> install I was only asked to install MySQL perl module (I installed it via
> CPAN).
> It's working like a cake.
>
> I discard there's a problem with the input VCF because I'm using exactly
> the input over the two environments (and the same one you used to test it
> yesterday)
>
> So my question is: Does VEP script use any other library, environment
> variable or tool which may be interfering?
>
> Best regards,
> Guillermo.
>
>
> On 04/06/15 09:32, Guillermo Marco Puche wrote:
>
> Hi again Will,
>
> I've completly cleaned PERL5LIB environment var. I've been testing
> changing between bioperl 1.2.3 and bioperl 1.6.1 and got same
> warnings/errors.
> I've cloned again all 79 API like you suggested in a new tmp location and
> included it in $PERL5LIB.
>
> *echo $PERL5LIB *
>
>
> /share/apps/local/bioperl-live:/share/gluster/tests/gmarco/tmp/ensembl/modules:/share/gluster/tests/gmarco/tmp/ensembl-funcgen/modules:/share/gluster/tests/gmarco/tmp/ensembl-variation/modules
>
> *ll /share/gluster/tests/gmarco/tmp*
>
> total 20
> drwxrwxr-x  8 gmarco users 4096 jun  4 08:44 ensembl
> drwxrwxr-x  8 gmarco users  146 jun  4 08:46 ensembl-funcgen
> drwxrwxr-x  5 gmarco users   64 jun  4 08:43 ensembl-tools
> drwxrwxr-x 10 gmarco users 4096 jun  4 08:45 ensembl-variation
>
> *perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl <http://variant_effect_predictor.pl> -i input.vcf -database --force_overwrite*
>
> 2015-06-04 09:29:13 - Starting...
> ERROR: Could not detect input file format
>
> If use the following flags  *-format vcf* *-vcf *then I start getting all
> those errors (see yesterday log).
>
> Is there any other Perl lib or requirement I could be missing? As I said
> it's very weird I have 0 problems with Ensembl 75 local API.
>
> Best regards,
> Guillermo.
>
> On 03/06/15 18:14, Will McLaren wrote:
>
> 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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>
>
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