<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Really only 560 Mb (Pine is 20 Gb by comparison). The single longest step for MAKER, is alignment which is done via BLAST. So the evidence dataset tends to be what can be filtered to get to a reasonable size. Protein alignments take long as they must be aligned against the 3 translated reading frames of the genome (so minimum 3x longer than DNA2DNA alignment, but in practice much much more). Alt_EST is even worse, as it must translate all 3 reading frames of the genome and all 3 of the data to be aligned (TBLASTX type alignment). So minimum 3x longer than protein alignment or 9X times longer than DNA2DNA alignment (but in practice much more). So the single best thing to do to reduce run time is to use protein evidence where possible instead of alt_EST evidence, or to ESTs from the same species and limit the use of proteins (ESTs from the same species are aligned as DNA2DNA, so it is very fast). Set all the blast_depth parameters in the maker_bopts.ctl file to 20 or 30. This will help if you have a very deep evidence dataset, by trimming overly deep alignment regions (less exonerate polishing).</div><div><br></div><div>Also you can try running MAKER on 40 cpus rather than 20 (basically doubling up even though you only have 20). This can work because, even though you gave MAKER 20 cpus to use, all 20 will rarely be using 100% of each CPU simultaneously. So launching 40 threads will give a slight boost in many instances by filling in the gaps when "wait" operations let cpus idle for a fraction of a second.</div><div><br></div><div>One good thing though, is that you only pay the price for data generation once. If you ever rerun with slightly modified parameters, MAKER is smart enough to reuse old results, so BLAST won't have to rerun.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Jasmin Zohren <<a href="mailto:j.zohren@qmul.ac.uk">j.zohren@qmul.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Friday, 10 May, 2013 1:07 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] annotation of birch genome<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:917517260;
mso-list-type:hybrid;
mso-list-template-ids:1122370140 -1697753630 134807555 134807557 134807553 134807555 134807557 134807553 134807555 134807557;}
@list l0:level1
{mso-level-start-at:0;
mso-level-number-format:bullet;
mso-level-text:-;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-font-family:Calibri;
mso-bidi-font-family:"Times New Roman";}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level3
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level4
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level5
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level6
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level7
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level8
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level9
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal">Dear Maker developers,<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">I am a PhD student at Queen Mary University in London working on tree genomics. I recently attended the GMOD conference in Cambridge and it was a pity that no one from the Maker side was there. But the two days were interesting anyway.<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">My current project is about birch which has just been sequenced and I now want to annotate it. Here are the details:<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><!--[if !supportLists]--><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman""> </span></span><!--[endif]-->Genome size: 560 Mb<o:p></o:p></p><p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><!--[if !supportLists]--><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman""> </span></span><!--[endif]-->Size of EST file (from a related species): 28 Mb<o:p></o:p></p><p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><!--[if !supportLists]--><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman""> </span></span><!--[endif]-->I am running it on a single node with 20 cores of 512 GB RAM (using “mpiexec -n 20 maker”)<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">I’ve also attached my maker_opts file with the parameters I am using. I assume the maker_bopts and maker_exe file are of minor importance for now.<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">My problem is, that the analysis is taking very long. It’s been running for weeks already and has only processed about 65 % of the scaffolds/contigs.<o:p></o:p></p><p class="MsoNormal">So I was wondering whether you have any suggestions how to speed things up. Especially as I intend to use Maker for other projects, too, and will also come back to the birch annotation once I have mRNA data for it.<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal">Many thanks in advance and kind regards,<o:p></o:p></p><p class="MsoNormal">Jasmin<o:p></o:p></p><p class="MsoNormal"><o:p> </o:p></p><p class="MsoNormal"><span style="mso-fareast-language:EN-GB">-----------------------------<o:p></o:p></span></p><p class="MsoNormal"><i><span style="mso-fareast-language:EN-GB">Jasmin Zohren<o:p></o:p></span></i></p><p class="MsoNormal"><i><span style="mso-fareast-language:EN-GB">PhD student in the INTERCROSSING ITN<o:p></o:p></span></i></p><p class="MsoNormal"><i><span style="mso-fareast-language:EN-GB">Queen Mary University of London<o:p></o:p></span></i></p><p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p><p class="MsoNormal"><i><span style="mso-fareast-language:EN-GB"><a href="http://intercrossing.wikispaces.com/">intercrossing.wikispaces.com</a><o:p></o:p></span></i></p><p class="MsoNormal"><i><span style="mso-fareast-language:EN-GB"><a href="http://evolve.sbcs.qmul.ac.uk/buggs/jasmin-zohren/">evolve.sbcs.qmul.ac.uk</a><o:p></o:p></span></i></p><p class="MsoNormal"><o:p> </o:p></p></div></div></div>_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>