<div dir="ltr">Thanks a lot. <div><br></div><div>I tried again. </div><div><br></div><div>As the result is the following :</div><div> => Only two lines error message.</div><div><br></div><div><div>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.</div><div><br></div><div>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.</div></div><div><br></div><div><br></div><div>  </div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Apr 10, 2015 at 5:27 PM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Namchul,<div><br></div><div>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.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Will</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 10 April 2015 at 02:15, namchul ghim <span dir="ltr"><<a href="mailto:chulghim@gmail.com" target="_blank">chulghim@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Sarah, <div><br></div><div>I use ensembl v79, GRCh37 latest version.</div><div>Exome annotation is very good.</div><div><br></div><div>This message happens in whole genome annotation. </div><div>many same messages are printed without any variant position information. </div><div><br></div><div><br></div><div>My running command is the following ...</div><div>    perl520/bin/perl  /mnt/lustre/Tools/VEP/src/ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -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  </div><div>-- 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<br></div><div><br></div><div><br></div><div><br></div><div>Error messages as the following ..  <br></div><div>It happens 217 count.</div><div><span style="font-size:12.8000001907349px">Use of uninitialized value in hash element at /mnt/lustre/Tools/VEP/src/</span><span style="font-size:12.8000001907349px">ensembl-tools-release-79/</span><span style="font-size:12.8000001907349px">scripts/variant_effect_</span><span style="font-size:12.8000001907349px">predictor/Bio/EnsEMBL/</span><span style="font-size:12.8000001907349px">Variation/VariationFeature.pm line 718.</span><br></div><div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">It happens  6 count.</div><div style="font-size:12.8000001907349px">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.</div></div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px"><div style="font-size:12.8000001907349px">It happens  2 count.</div></div><div>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.</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 9, 2015 at 6:44 PM, Sarah Hunt <span dir="ltr"><<a href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    <br>
    Hi Namchul,<br>
    <br>
    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?<br>
    <br>
    Thanks,<br>
    <br>
    Sarah<div><div><br>
    <div><br>
      On 09/04/2015 02:20, namchul ghim wrote:<br>
    </div>
    </div></div><blockquote type="cite"><div><div>
      <div dir="ltr">
        <div>I got the following error message during annotating  whole
          genome vcf file.</div>
        <div>These messages doesn't affect the result.  is it right?</div>
        <div><br>
        </div>
        <div> <br>
        </div>
        <div>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.</div>
        <div><br>
        </div>
        <div>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.</div>
        <div><br>
        </div>
        <div><br>
        </div>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      </div></div><pre>_______________________________________________
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    <br>
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