[ensembl-dev] Warning message in from VariationFeature.pm

[Duarte Molha]

I believe the main problem is that this Variation feature, for some reason
does not have a splice attached to it : 'slice' => undef

so the method to extract the slice and expand


471:                my $slice = $self->feature_Slice->expand(
472:                    MAX_DISTANCE_FROM_TRANSCRIPT,
473:                    MAX_DISTANCE_FROM_TRANSCRIPT
474:                );

Fails.

Anyone knows what might be causing this?

Best regards

Duarte



=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================


On Wed, Jul 31, 2013 at 5:05 PM, Duarte Molha <duartemolha at gmail.com> wrote:

> In an effort to understand better what might be causing this ... here is a
> dumb of one such object causing the error message:
>
> the VCF line:
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
>  sample-01  sample-02  sample-03 sample-04 sample-05 sample-06
> 1 I777437 I. IA IC I667.93 IPASS
> IAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2
> IGT:AD:DP:GQ:PL I0/0:60,0:60:99:0,138,1819 I0/0:82,0:82:99:0,205,2614
> I0/1:52,28:80:99:706,0,1290 I0/0:100,0:100:99:0,253,3074
> I0/0:83,0:83:99:0,178,2360 I0/0:82,0:82:99:0,166,2135
>
> at line 471 of /Bio/EnsEMBL/Variation/VariationFeature.pm
>
> my object $self contains:
>
> 0  Bio::EnsEMBL::Variation::VariationFeature=HASH(0x57802b0)
>    '_line' =>
> "1\cI777437\cI.\cIA\cIC\cI667.93\cIPASS\cIAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2\cIGT:AD:DP:GQ:PL\cI0/0:60,0:60:99:0,138,1819\cI0/0:82,0:82:99:0,205,2614\cI0/1:52,28:80:99:706,0,1290\cI0/0:100,0:100:99:0,253,3074\cI0/0:83,0:83:99:0,178,2360\cI0/0:82,0:82:99:0,166,2135"
>    'adaptor' =>
> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor=HASH(0x4b06030)
>       '_is_multispecies' => ''
>       'db' => Bio::EnsEMBL::Variation::DBSQL::DBAdaptor=HASH(0x52b4f08)
>          '_dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)
>             '_dbname' => 'homo_sapiens_variation_72_37'
>             '_driver' => 'mysql'
>             '_host' => 'ensembldb.ensembl.org'
>             '_port' => 5306
>             '_query_count' => 4
>             '_timeout' => 0
>             '_username' => 'anonymous'
>             'connected32406' => 1
>             'db_handle32406' => DBI::db=HASH(0x51e5ee8)
>                  empty hash
>             'reconnect_when_lost' => 1
>          '_group' => 'variation'
>          '_is_multispecies' => ''
>          '_no_cache' => 1
>          '_species' => 'homo_sapiens'
>          '_species_id' => 1
>       'dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)
>          -> REUSED_ADDRESS
>       'species_id' => 1
>    'allele_string' => 'A'
>    'chr' => 1
>    'end' => 777437
>    'existing' => ARRAY(0x10861900)
>         empty array
>    'genotype' => ARRAY(0x577ff80)
>       0  'A'
>       1  'A'
>    'individual' => 'sample-01'
>    'map_weight' => 1
>    'non_variant' => 1
>    'phased' => 1
>    'slice' => undef
>    'start' => 777437
>    'strand' => 1
>    'variation_name' => '1_777437_A'
>
>
>
>
> =========================
>      Duarte Miguel Paulo Molha
>          http://about.me/duarte
> =========================
>
>
> On 31 July 2013 13:52, Duarte Molha <duartemolha at gmail.com> wrote:
>
>> Hi Devs
>>
>>  I have been trying to run a VCF file by the variant annotation script
>> and I've been getting a warning message that I have never before
>> encountered..
>>
>>  I was wondering if someone could let me know if it is something I am
>> doing wrong…
>>
>>  The message is :
>>
>>  *Can't call method "expand" on an undefined value at
>> <sic>/Bio/EnsEMBL/Variation/VariationFeature.pm line 471*
>>
>> **
>>
>> * *
>>
>> Here are the configuration options I am using:
>>
>>
>>
>> Configuration options:
>>
>>  ###
>>
>> allow_non_variant    1
>>
>> cache                1
>>
>> canonical            1
>>
>> ccds                 1
>>
>> check_alleles        1
>>
>> check_existing       1
>>
>> config               vep_human.ini
>>
>> core_type            core
>>
>> custom
>> ./vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
>> ./vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact
>>
>> db_version           72
>>
>> dir                  /ReferenceData/vep_cache
>>
>> dir_cache            /ReferenceData/vep_cache
>>
>> dir_plugins          ./Plugins
>>
>> domains              1
>>
>> force_overwrite      1
>>
>> fork                 5
>>
>> gmaf                 1
>>
>> hgnc                 1
>>
>> host                 ensembldb.ensembl.org
>>
>> individual           all
>>
>> input_file           All_BOTH_SNPINDELfilter_PASSED.vcf
>>
>> maf_1kg              1
>>
>> numbers              1
>>
>> output_file          All_BOTH_SNPINDELfilter_PASSED.ann
>>
>> plugin
>> OGT_NHBLI_MAF,/ReferenceData/NHLBI_EVS/NHLBI_OGT.gz
>> OGT_selected_VCF_fields_output  Blosum62        Carol   OGT_Condel,b
>> OGT_Grantham    TSSDistance     Downstream
>>
>> polyphen             b
>>
>> port                 5306
>>
>> protein              1
>>
>> regulatory           1
>>
>> sift                 b
>>
>> species              homo_sapiens
>>
>> stats                HASH(0x4370ad8)
>>
>> terms                SO
>>
>> verbose              1
>>
>>
>>
>> I would be very grateful for your help.
>>
>>  Duarte Molha
>>
>
>
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