[ensembl-dev] About "Use of uninitialized value message ~~~~"

Will McLaren wm2 at ebi.ac.uk
Fri Apr 10 09:27:44 BST 2015


Hi Namchul,

Thanks for reporting this; we've put in a fix so the warning won't appear
any more (you can re-run INSTALL.pl to update your API), but you shouldn't
worry about any effect on your results.

Will

On 10 April 2015 at 02:15, namchul ghim <chulghim at gmail.com> wrote:

> Hello Sarah,
>
> I use ensembl v79, GRCh37 latest version.
> Exome annotation is very good.
>
> This message happens in whole genome annotation.
> many same messages are printed without any variant position information.
>
>
> My running command is the following ...
>     perl520/bin/perl
>  /mnt/lustre/Tools/VEP/src/ensembl-tools/scripts/variant_effect_predictor/
> variant_effect_predictor.pl -i /mnt/lustre/Tools/VEP/20150410/new/wg_va
>                                 rinat/5.vcf --cache --offline --everything
> --force_overwrite --dir /mnt/lustre/Tools/VEP/cache/GRCh37_RefSeq -o
> /mnt/lustre/Tools/VEP/20150410/new/wg_varinat/5.vcf  --vcf --species
> homo_sapiens --xref_refseq  -regulatory --flag_pick  --buffer_size 4000
> --fork 4  --hgvs --force --fasta
> /mnt/lustre/Tools/VEP/cache/GRCh37_RefSeq/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
>
> -- custom /cache/GRCh37_RefSeq/clinvar/clinvar.vcf.gz,CLINVAR
>
>  ,vcf,exact,0,RS,RSPOS,RV,VP,GENEINFO,dbSNPBuildID,SAO,SSR,WGT,VC,PM,TPA,PMC,S3D,SLO,NSF,NSM,NSN,REF,SYN,U
>
>  3,U5,ASS,DSS,INT,R3,R5,OTH,CFL,ASP,MUT,VLD,G5A,G5,HD,GNO,KGPhase1,KGPhase3,CDA,LSD,MTP,OM,NOC,WTD,NOV,CAF
>
>  ,COMMON,CLNHGVS,CLNALLE,CLNSRC,CLNORIGIN,CLNSRCID,CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC
>  --custom
> /cache/GRCh37_RefSeq/ESP6500/ESP6500.vcf.gz,ESP6500,vcf,exact,0,DBSNP,EA_AC,AA_
>
>  AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,AA,FG,HGVS_CDNA_VAR,HGVS_PROTEIN_VAR,CDS_SIZES,PH,CP,CG,GL,GS,CA,EXOM
>
>  E_CHIP,GWAS_PUBMED,EA_AGE,AA_AGE,GRCh38_POSITION
>
>
>
> Error messages as the following ..
> It happens 217 count.
> Use of uninitialized value in hash element at /mnt/lustre/Tools/VEP/src/
> ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/VariationFeature.pm
> line 718.
>
> It happens  6 count.
> Use of uninitialized value $stable_id in pattern match(//m) at
> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 670.
>
> It happens  2 count.
> Use of uninitialized value in pattern match (m//) at
> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/s
>
>  cripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm line
> 2560.
>
>
>
>
>
>
>
>
>
>
>
>
> On Thu, Apr 9, 2015 at 6:44 PM, Sarah Hunt <seh at ebi.ac.uk> wrote:
>
>>
>> Hi Namchul,
>>
>> The message may indicate missing results. Could you supply more
>> information on how you are using VEP? I assume you are using one of the
>> release79 caches? Do you have any examples of VCF lines triggering the
>> message?
>>
>> Thanks,
>>
>> Sarah
>>
>>
>> On 09/04/2015 02:20, namchul ghim wrote:
>>
>>  I got the following error message during annotating  whole genome vcf
>> file.
>> These messages doesn't affect the result.  is it right?
>>
>>
>>  Use of uninitialized value in hash element at
>> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/VariationFeature.pm
>> line 718.
>>
>>  Use of uninitialized value $stable_id in pattern match(//m) at
>> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>> line 670.
>>
>>
>>
>>
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>
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