<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><div><font face="Calibri,sans-serif">Hi Ambrose,</font></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">It is likely caused by an issue with hints being generated for Fgenesh, I’ve attached an updated module to be placed here —></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">.../maker/lib/Widget/fgenesh.pm.</div></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">I will also integrate this into the MAKER download.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Ambrose Andongabo (RRes-Roth)" <<a href="mailto:Ambrose.Andongabo@rothamsted.ac.uk">Ambrose.Andongabo@rothamsted.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Thursday, January 23, 2014 at 4:19 AM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] MAKER annotation and Trinity output<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Dear all,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">I am using the latest version of MAKER and I keep on getting this error message when I activate fgenesh gene predictor in the maker_opts.ctl file. It runs successfully
when using SNAP, GeneMark and AUGUSTUS. If I do not provide my ESTs evidence in the form of Trinity output, the pipeline will run successfully using all the four gene predictors including fgenesh.
</span> <span style="color:#1F497D"> I wonder if someone encountered such a problem before<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">#--------- command -------------#<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Widget::fgenesh:<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">/home/data/MAKER_2.30/maker/bin/../lib/Widget/fgenesh/fgenesh_wrap /home/data/mg_annotation/fgenesh/fgenesh /home/data/mg_annotation/fgenesh/Fusarium /tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.fgenesh.fasta
-exon_table:/tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.xdef.fgenesh > /tmp/maker_cAePfY/0/164_0.557-1163.Fusarium.auto_annotator.fgenesh<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">#-------------------------------#<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">ERROR: FGENESH Failed<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">ERROR: FgenesH failed<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">--> rank=NA, hostname=vnc.rothamsted.ac.uk<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">ERROR: Failed while annotating transcripts<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">ERROR: Chunk failed at level:1, tier_type:4<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">FAILED CONTIG:contig_1<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">ERROR: Chunk failed at level:6, tier_type:0<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">FAILED CONTIG:contig_1<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">examining contents of the fasta file and run log<o:p></o:p></span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></b></p><p class="MsoNormal"><span style="color:#1F497D">I will be grateful for your contribution<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="color:#1F497D">Thanks<o:p></o:p></span></p><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal"><span style="color:#1F497D">Ambrose</span><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p></o:p></span></b></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p></div><br>--
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