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

[namchul ghim]

Thanks a lot.

I tried again.

As the result is the following :
 => Only two lines error message.

Use of uninitialized value in pattern match (m//) at
/mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 2561.

Use of uninitialized value in pattern match (m//) at
/mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 2561.















On Fri, Apr 10, 2015 at 5:27 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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>
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