[ensembl-dev] VEP 79 API problems
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Thu Jun 4 12:27:11 BST 2015
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
> <mailto: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 <http://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
>>> <http://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
>>> <mailto: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
>>>> <mailto: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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