[ensembl-dev] VEP 79 API problems

Will McLaren wm2 at ebi.ac.uk
Thu Jun 4 14:16:49 BST 2015


Sorry Guillermo, I'm running out of ideas.

Does the test unit run OK?

perl
ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t

Will
On 4 Jun 2015 12:27, "Guillermo Marco Puche" <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hi Will,
>
> I'm getting the exact same error with example_GRCh37.vcf:
>
> ERROR: Could not detect input file format
>
>
> I've made a test script as you suggest with the following code and I don't
> get any error:
>
> #!/usr/bin/env perl
>
> use strict;
> use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);
>
>
> Regards,
> Guillermo.
>
> On 04/06/15 13:12, Will McLaren wrote:
>
> 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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