<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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