<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ian - <div><br></div><div>Do you get any gene models if you run RM or SNAP on these directly? I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?</div><div><br></div><div>Jason<br><div><div>On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins. I have looked through the output from the run and of the 74 contigs that failed I only have three errors.<br><br>They are Chunk failed at level 3, 8, & 16<br><br>What are those errors? How can I get the annotations for these failed runs to work? I have the entire output if you would need to see that file. In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time. All 74 contigs failed all 3 attempts to run. Any help would be much appreciated.<br><br>Cheers<br>Ian<br><br><br>*************************************<br>Mr. Ian Misner<br>PhD. Candidate<br>Department of Biological Sciences<br>University of Rhode Island<br>120 Flagg Road<br>Kingston, RI 02881<br>Office: CBLS 260<br>Ph: 1-401-874-9726<br>fax (401) 874-2065<br><a href="mailto:ianmisner@my.uri.edu">ianmisner@my.uri.edu</a><br>http://cels.uri.edu/bio/lanelab/ <br><br><br><br><br><br><br><br><br>_______________________________________________<br>maker-devel mailing list<br>maker-devel@box290.bluehost.com<br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div>Jason Stajich</div><div><a href="mailto:jason.stajich@gmail.com">jason.stajich@gmail.com</a></div><div><a href="mailto:jason@bioperl.org">jason@bioperl.org</a></div></span>
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