<div dir="ltr">Hi Matteo,<div><br></div><div>Strange - the subroutine containing that code should only be triggered with the --debug flag active.</div><div><br></div><div>Perhaps you have a vep.ini file present with the debug flag active? I can't see any other way it is being triggered.</div><div><br>In any case, the warning is harmless!</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 23 May 2016 at 13:29, Matteo <span dir="ltr"><<a href="mailto:matteodeg@gmail.com" target="_blank">matteodeg@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 bgcolor="#FFFFFF" text="#000000">
    Hi Will,<br>
    <br>
    I don't use --debug option in my command line, I only use these
    flags:<br>
    <br>
        --cache \<br>
        --assembly GRCh37 \<br>
        --offline \<br>
        --force_overwrite \<br>
        -v \<br>
        --variant_class \<br>
        --sift b \<br>
        --poly b \<br>
        --vcf_info_field ANN \<br>
        --hgvs \<br>
        --protein \<br>
        --canonical \<br>
        --check_existing \<br>
        --gmaf \<br>
        --pubmed \<br>
        --species homo_sapiens \<br>
        --failed 1 \<br>
        --plugin LoFtool \<br>
        --vcf<br>
    <br>
    Thank you,<br>
    <br>
    matteo<div><div class="h5"><br>
    <br>
    <div>Il 23/05/2016 13:58, Will McLaren ha
      scritto:<br>
    </div>
    <blockquote type="cite">
      <div dir="ltr">Hi Matteo,
        <div><br>
        </div>
        <div>Remove the --debug flag from your command line; this is
          intended for use only by VEP developers.</div>
        <div><br>
        </div>
        <div>Regards</div>
        <div><br>
        </div>
        <div>Will McLaren</div>
        <div>Ensembl Variation</div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On 23 May 2016 at 12:35, Matteo <span dir="ltr"><<a href="mailto:matteodeg@gmail.com" target="_blank">matteodeg@gmail.com</a>></span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
            I'm using the last VEP version (84).<br>
            I get this error:<br>
            <br>
            Negative repeat count does nothing at
            ~/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
            line 6906.<br>
            [>                                              ]    [ 0%
            ]Negative repeat count does nothing at
            /home/jarvis/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
            line 6906.<br>
            [>                                              ]    [ 0%
            ]Negative repeat count does nothing at
            /home/jarvis/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
            line 6906.<br>
            [===============================================]  [ 100% ]<br>
            <br>
            However, the annotation seems to be ok. Any idea?<br>
            Thanks,<br>
            <br>
            Matteo<br>
            <br>
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          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      <pre>_______________________________________________
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</pre>
    </blockquote>
    <br>
  </div></div></div>

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<br></blockquote></div><br></div>