<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Did you email the genemark authors? They would be a better source for help.<div> I experienced the same problems with the yeast data to train from and didn't use genemark for those species - it may be that it is expecting more introns and the files for training are empty on some rounds. </div><div><br><div>Jason<br><div><div>On Apr 12, 2013, at 5:47 AM, xu zhang <<a href="mailto:xzhang@genome.wustl.edu">xzhang@genome.wustl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I know how to do that. I tried different initial mod file and it worked on my sequences with org_S1_55.0mtx initial mod. I don't know why. if somebody knows, please let me know.<br><br>Thanks,<br>Xu<br><br>On 04/10/2013 11:30 AM, xu zhang wrote:<br><blockquote type="cite">Hi All,<br><br>Does anybody have genemark .mod file for yeast? I tried to create my own model file using this command" gm_es.pl S288C_reference_sequence_R64-1-1_20110203.fsa", where the sequence was downloaded from ncbi". it failed with this error "<br>warning, error in input file format:<br>-3<br>error reading parameter BRANCH_MAT<br>error in model file /gscmnt/gc2124/info/annotation/personal_dir/xzhang/yeast/s_cerevisiae/genemark/training2/mod/es.mod<br>Error on system: prediction step" and "Error: unknown line format".<br><br>and I tried the sample file(pythium_ultimum_scaffolds.fasta) from Carson. a mod file was created, although it also had some error information<br>" warning, error in input file format:<br>-13<br>5654 dna.fa.good.gb.acc.ph2<br>first order for ACC 2<br>Error: unknown line format<br> GC% ntron".<br><br>any suggestion and comments are appreciated<br><br>Thanks,<br>Xu<br><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></blockquote><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></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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