[ensembl-dev] VEP 79 API problems
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Thu Jun 4 14:47:35 BST 2015
Hi Will,
I've been comparing variant_effect_predictor script from version 75 vs 79.
After adding a few prints to VEP.pm inside I've spotted the bug. However
I cannot resolve it.
Those lanes are new from 75 to 79 in VEP script (175 and 176):
*
*
* # split again to avoid Windows character nonsense*
* foreach my $line(split /\r|\R/) {*
I've checked that script is spliting line each time it finds a capital R
in VCF file as identifying it as a newline character from Windows. I
can't reproduce it in virtual machine since its a fresh Linux install.
In my work environment I'm getting this kind of bug, so I guess it has
something to do with file enconding or locale? Has anyone else
experienced this?
Now I know where's the error but I've no idea how to solve it.
Regards,
Guillermo.
On 04/06/15 15:16, Will McLaren wrote:
>
> 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
> <mailto: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
>> <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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