[ensembl-dev] VEP 79 API problems
Will McLaren
wm2 at ebi.ac.uk
Thu Jun 4 16:49:34 BST 2015
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> 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> 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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