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

[namchul ghim]

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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