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

[Duarte Molha]

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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