<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="">Most of the parameters affect the command line used to run blast/exonerate. In that case it will rerun. Some like the percent coverage parameter are post run filters. For those, it just re-parses. I don’t remember off the top of my head which ones fall into which category, but most fall into the first one.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 6, 2017, at 1:18 AM, Ray Cui <<a href="mailto:rcui@age.mpg.de" class="">rcui@age.mpg.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="auto" class="">Hi Carson,<div dir="auto" class=""><br class=""></div><div dir="auto" class=""> Yet another question: if I change the blast and exonerate parameters in the bopts file, will maker automatically rerun blast and exonerate (or, parse the existing output with the new cutoffs)?</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Thanks</div><div dir="auto" class="">Ray </div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Apr 5, 2017 6:01 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Augustus can sometimes produce alternate models. It normally only happens with hints and not with the raw prediction though. MAKER by default will only keeps the best scoring one (scored by AED). But EVM technically gets to see all of the raw models. Its the kind of thing where I would have to have the exact data and contig you used to run to see if this is something easily pulled apart for EVM.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 5, 2017, at 6:57 AM, Ray Cui <<a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a>> wrote:</div><br class="m_-3757697847264070654Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Carson,<div class=""><br class=""></div><div class=""> I think I found the reason for this here <a href="https://sourceforge.net/p/evidencemodeler/mailman/message/27284428/" target="_blank" class="">https://sourceforge.net/<wbr class="">p/evidencemodeler/mailman/<wbr class="">message/27284428/</a> . </div><div class=""> These messages are from EVM. The second type of message is due to incomplete gene models, so it's not a big deal. The first type is because of the overlapping gene models predicted by Augustus. This is a bit strange. Does maker allow Augustus to produce alternative spliced variants?</div><div class=""><br class=""></div><div class="">Best Regards,</div><div class="">Ray</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3757697847264070654gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dr. Rongfeng (Ray) Cui</div><div class="">Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing</div><div class=""><span style="text-align:justify" class="">Wissenschaftlicher MA</span> / Postdoctoral researcher</div><div class="">Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne</div><div class="">Postal address: Postfach 41 06 23, D-50866 Köln / Cologne</div><div class="">Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496</a> </div><div class="">Mobile: +49 <a value="+4922137970496" style="color:rgb(17,85,204)" class="">0221 37970 496</a></div><div class=""><a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a></div><div class=""><a href="http://www.age.mpg.de/" target="_blank" class="">www.age.mpg.de</a> </div><div class=""><br class=""></div></div><div class=""><br class=""></div></div><div class=""></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Wed, Apr 5, 2017 at 1:33 PM, Ray Cui <span dir="ltr" class=""><<a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Carson,<div class=""><br class=""></div><div class=""> I saw these messages in the log, is this a concern? I'm using Maker beta 3.</div><div class=""> Message 1:</div><div class=""><br class=""></div><div class=""><div class="">Error with prediction: augustus_masked lend_intergenic: 730288, rend_intergenic: 664875 at /beegfs/group_dv/software/sour<wbr class="">ce/EVidenceModeler-1.1.1/<a href="http://evidence_modeler.pl/" target="_blank" class="">evide<wbr class="">nce_modeler.pl</a> line 3218.</div><div class=""><br class=""></div><div class=""> Message 2:</div><div class=""><div class="">Sorry, prediction pred_gff:gth_m.PLPscf119:hit:7<wbr class="">108:43932 fails validation.</div><div class="">(GTT) TA 683590-683765 GC ATG</div><div class="">(GCA) AG 701228-701409 GT AGG</div><div class="">(GGA) AG 704938-705037 GT AGG</div><div class="">(GGC) AG 721672-721792 GT AGG</div><div class="">(TTG) AG 730110-730288 AC GAA</div><div class="">-recovered pred_gff:gth_m.PLPscf119:hit:7<wbr class="">108:43932, terminal, 730110, 730288</div><div class="">-recovered pred_gff:gth_m.PLPscf119:hit:7<wbr class="">108:43932, internal, 701228, 701409</div><div class="">-recovered pred_gff:gth_m.PLPscf119:hit:7<wbr class="">108:43932, internal, 704938, 705037</div><div class="">-recovered pred_gff:gth_m.PLPspolishing proteins</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> PS: I am still keep being kicked out of the maker mailing list due to some reason, if you can forward the msg. there it would be great.</div><div class=""> </div><div class="">Best Regards,</div><div class="">Ray</div><div class=""><br class=""></div><div class=""><div class="m_-3757697847264070654m_6008983587976084041gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dr. Rongfeng (Ray) Cui</div><div class="">Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for Biology of Ageing</div><div class=""><span style="text-align:justify" class="">Wissenschaftlicher MA</span> / Postdoctoral researcher</div><div class="">Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne</div><div class="">Postal address: Postfach 41 06 23, D-50866 Köln / Cologne</div><div class="">Tel.:<a href="tel:+49%20221%20496" value="+49221496" target="_blank" class="">+49 (0)221 496</a> </div><div class="">Mobile: +49 <a value="+4922137970496" style="color:rgb(17,85,204)" class="">0221 37970 496</a></div><div class=""><a href="mailto:rcui@age.mpg.de" target="_blank" class="">rcui@age.mpg.de</a></div><div class=""><a href="http://www.age.mpg.de/" target="_blank" class="">www.age.mpg.de</a> </div><div class=""><br class=""></div></div><div class=""><br class=""></div></div><div class=""></div></div></div></div></div></div></div></div>
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