[ensembl-dev] VEP 79 API problems
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Thu Jun 4 17:02:12 BST 2015
Hello Will,
Wrong behavior machine has Centos 5.4 and Perl v5.8.8 built for
x86_64-linux-thread-multi.
So should I completly remove ?
* foreach my $line(split /\r|\R/) {*
I was thinking about just removing \R from regex.
Regards,
Guillermo.
On 04/06/15 17:49, Will McLaren wrote:
> Thanks
>
> I had forgotten about that change. You could just edit the script and
> change or even remove the regexp:
>
> foreach my $line(($_)) {
>
> What's your Perl version and system architecture? I'm surprised this
> has not caught anyone else out.
>
> Will
>
> On 4 June 2015 at 14:47, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> 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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>>>>>
>>>>>
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