<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="">Also it’s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 24, 2016, at 7:22 PM, Jason Stajich <<a href="mailto:jason.stajich@gmail.com" class="">jason.stajich@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="white-space:pre-wrap" class="">the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. </div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <<a href="mailto:sullis02@nyu.edu" class="">sullis02@nyu.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Sorry if this is a dumb question.<div class=""><br class=""></div><div class="">Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input<div class=""><br class=""></div><div class="">I generated a training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species. I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):</div><div class=""><br class=""></div><div class=""><p style="padding: 0px; margin: 8px 0px; line-height: 1.3em; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 11.2011px;" class=""><br class=""></p></div><div class=""><div class=""><b class="">Species parameter archive</b>: parameters.tar.gz</div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">Training genes: </b> training.gb.gz</div><div class=""><br class=""></div><div class=""><b class="">Ab initio predictions</b>: ab_initio.tar.gz</div><div class=""><br class=""></div><div class=""><b class="">predictions with hints:</b> hints_pred.tar.gz</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">The 'training genes' (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.</div><div class=""><br class=""></div><div class="">the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.</div><div class=""><br class=""></div><div class="">Do you know which file would be correct for input to online MAKER as a 'model' file?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">(NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br clear="all" class=""><div class=""><br class=""></div><div data-smartmail="gmail_signature" class=""><br class=""></div>
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