<div dir="ltr">Hi Wei, Konrad,<div><br></div><div>From the code it looks as if this is giving this warning when exon_number is not defined. This can be the case if the variant does not fall in an exon, so the plugin should really be checking if it is defined before you attempt to split it.</div><div><br></div><div>On the other hand, my guess is by that point in the code you would hope to be only operating on exonic variants, so either the variant that is causing the warning is being called exonic when it isn't, or it is exonic and the exon_number routine isn't working properly.</div><div><br></div><div>The only situation I can think of that might be the case is if the variant falls in one of the very rare frameshift introns that occur in some Ensembl transcripts. These are very short (<=12bp) artificial introns that are introduced into a transcript's structure in order to make the structure, genome sequence and transcript evidence play nicely together.</div><div><br></div><div>If either of you do track down a variant that causes this, and there is something to fix on the VEP side, please let us know.</div><div><br></div><div>Regarding capturing errors, VEP does capture it's own warnings via the warning_msg() subroutine (they can be directed to STDERR or any output file), but I don't think it can capture warnings like this. Plugins are run in an eval block, so errors are caught (and reported via warning_msg()), but I don't think it can capture warnings like this.</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 10 March 2016 at 17:05, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Hi Wei,</div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">We've had this issue sporadically as well, but we have not yet been able to pinpoint the variants that cause this error. It's on our todo list to fix, but it seems rare enough and hasn't been prominent enough to get noticed in any manual inspections that we do.</div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">On that note, Ensembl dev folk/Will, is there a way in VEP to provide a bit more error logging? I should have asked this a long time ago, but it would be great to have a logging level that would print which variant an error happens on.</div> <div><br></div> <div><div style="font-family:helvetica,arial;font-size:13px">-Konrad</div></div><div><div class="h5"> <br><p>On March 10, 2016 at 11:57:21 AM, Wei Zhao (<a href="mailto:mikezhaow@gmail.com" target="_blank">mikezhaow@gmail.com</a>) wrote:</p> </div></div><blockquote type="cite"><span><div><div></div><div><div><div class="h5">
<div dir="ltr">Dear LOFTEE plugin developers,<br>
<br>
I met with this error message when I was using the LOFTEE
plugin:<br>
<br>
"Use of uninitialized value in split at .vep/Plugins/LoF.pm line
378"<br>
<br>
Both VEP and LOFTEE ran smoothly without a problem. But I
just saw this error message in the error files returned by our
clusters' queuing system. Just want to know if this is
something I should worry about. Thank you for your kind
help!<br>
<br>
I am currently using VEP v83 and Perl v5.20.1.<br>
<br>
Best,<br>
Wei</div></div></div>
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