[ensembl-dev] About "Use of uninitialized value message ~~~~"
Will McLaren
wm2 at ebi.ac.uk
Mon Apr 13 16:26:10 BST 2015
Again, this is not one to worry about.
We're looking into the cause of the warning.
Regards
Will
On 13 April 2015 at 02:26, namchul ghim <chulghim at gmail.com> wrote:
> 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.
>
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> 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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