[ensembl-dev] VEP 79 API problems

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Thu Jun 4 08:32:31 BST 2015 

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 -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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