<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">est2genome only works with the data given to est=.<br class=""><div><br class=""></div><div>For the second error, you must provide the path of the evm executable in maker_exe.ctl. It apparently was not in your PATH, so it didn’t get automatically filled out.</div><div><br class=""></div><div>Here is an example from the wiki of using est2genome and protein2genome to train SNAP for the next MAKER run —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Training_ab_initio_Gene_Predictors</a></div><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 24, 2018, at 3:28 AM, Linnie Linnie <<a href="mailto:peachandolives@gmail.com" class="">peachandolives@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Hi,</div><div class=""><br class=""></div><div class="">I am trying to run maker together with EVM. I want to annotate a genome for which there is no evidence data, which is why I am using ESTs and protein data from a closely related species. I am finding two unrelated issues.</div><div class=""><br class=""></div><div class="">The first one is the following: <br class=""></div><div class="">I set up the control files passing alt_est with a fasta file of ESTs, protein with protein from a closely related species as well as uniprot-sprot.fa, es2genome=1 and prot2genome=1. I am getting the following error:</div><div class=""><br class=""></div><div class="">>ERROR: You must provide some form of EST evidence to use est2genome as a predictor.</div><div class=""><br class=""></div><div class="">Does this mean I can only use est2genome with ESTs from the species of interest?</div><div class=""><br class=""></div><div class="">The second error relates to EVM:</div><div class="">I have passed in the file maker_opts.ctl the option run_evm=1. I have used default parameters in the file maker_evm.ctl. I am getting the following error:<br class=""></div><div class=""><br class=""></div><div class="">>ERROR: You have failed to provide a value for 'evm' in the control files.</div><div class=""><br class=""></div><div class="">Does this error relate to the maker_opts.ctl file or the maker_evm.ctl one? How could I fix it?<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">And lastly, a more general but fundamental question. Is my approach sensible? My plan is to run this evidence-based annotation, then perhaps train SNAP, Augustus and GeneMark, and use those output files to re-run maker with ab-initio parameters.</div><div class=""><br class=""></div><div class="">I would appreciate any input on any of these issues.</div><div class=""><br class=""></div><div class="">Thank you!</div><div class=""><br class=""></div><div class=""><br class=""></div></div></div></div></div>
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