<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Jason,<div class=""><br class=""></div><div class="">It could be a couple of things. If you have a cut down version of your gff3 that I can use to recreate the error I can debug it. The quality_filter.pl script is still a pretty young accessory script, so you may have something in your file that It wasn’t tested against.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike</div><div class=""><br class=""></div><div class=""> </div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 3, 2015, at 2:48 PM, Jason Gallant <<a href="mailto:jgallant@msu.edu" class="">jgallant@msu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Mike (list copied for future reference),<div class=""><br class=""></div><div class="">I found your very nice protocols paper on using Maker from 2014. I’ve been following it to the letter as I’m wrapping up my annotation project.</div><div class=""><br class=""></div><div class="">I’ve located your <a href="http://quality_filter.pl/" class="">quality_filter.pl</a> script and am using it on my GFF files to create maker standard and maker default data sets from my maker-max GFF file. I’m noticing that perl complains a lot while this is running about “use of uninitialized value”. This occurs on two separate passes as far as I can tell. When generating the “maker standard” file, it occurs for many lines in my GFF file as:</div><div class=""><br class=""></div><div class="">Use of uninitialized value $array[2] in pattern match (m//) at /mnt/home/jgallant/<a href="http://quality_filter.pl/" class="">quality_filter.pl</a> line 50, <GEN0> line Y.<br class=""></div><div class=""><br class=""></div><div class="">And then later it complains again with a similar message</div><div class=""><br class=""></div><div class="">Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" class="">quality_filter.pl</a> line 92, <GEN1> line X.<br class=""></div><div class="">Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" class="">quality_filter.pl</a> line 96, <GEN1> line X.<br class=""></div><div class="">Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/<a href="http://quality_filter.pl/" class="">quality_filter.pl</a> line 100, <GEN1> line X<br class=""></div><div class=""><br class=""></div><div class="">Any insights as to what causes this? I seem to get a fully formed GFF3 file out the other side, but the command line fills with these messages and makes me nervous that something isn’t right.</div><div class=""><br class=""></div><div class="">I’d appreciate any thoughts!</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Jason Gallant</div></div>
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