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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thanks Carson, very helpful. We will investigate further.<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Carson Holt <carsonhh@gmail.com>
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<b>Sent:</b> 23 October 2019 19:11<br>
<b>To:</b> David Hughes <david.hughes@rothamsted.ac.uk>; Maker Mailing List <maker-devel@yandell-lab.org><br>
<b>Subject:</b> Re: maker-devel post from david.hughes@rothamsted.ac.uk requires approval<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">MAKER will use the files that you provide on the command line in the order they are provided. It will not check the names, it will just read them in one at a time and add their internal options in the order they are encountered. If no files
are provided on the command line, then it will open the following files in order if they exist in the working directory: maker_opts.ctl, maker_bopts.ctl, maker_exe.ctl, and maker_evm.ctl.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If the same option is supplied twice, subsequent values will override and replace the first. The est2genome=1 option will not cause other values to be ignored or altered. However if you use the hidden and undocumented est_forward=1 option,
it will override a number of internal values.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">—Carson<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#7F7F7F">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">David Hughes <</span><a href="mailto:david.hughes@rothamsted.ac.uk"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">david.hughes@rothamsted.ac.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#7F7F7F">Subject:<span class="apple-converted-space"> </span></span></b><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">MAKER v3.0.0.</span></b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#7F7F7F">Date:<span class="apple-converted-space"> </span></span></b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">October 23, 2019 at 8:24:24 AM
MDT<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#7F7F7F">To:<span class="apple-converted-space"> </span></span></b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">"</span><a href="mailto:maker-devel@yandell-lab.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">maker-devel@yandell-lab.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">"
<</span><a href="mailto:maker-devel@yandell-lab.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">maker-devel@yandell-lab.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px">
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<p class="MsoNormal">When we set est2genome=1 in maker_opts.transfer.ctl, we find that maker_bopts.ctl seems not to be used.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Instead, maker_bopts.log sets ep_score_limit=10 and en_score_limit=20 and will not us change these parameters.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Is this intended? Very grateful for your advice<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.
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