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Hi Jose, the time it takes maker to annotate a genome depends greatly on the hardware setup (as you pointed out, processors, memory, etc) as well as the size of the genome and the size and type of the datasets you use to annotate the genome (numerous RNAseq
datasets for example will take longer than a project without any RNAseq data).
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<div class="">However, the MPI parallelization implemented in MAKER guarantees that the runtime should scale linearly with the number of processors allotted to the MAKER run. This is explained in the MAKER2 paper (Holt and Yandell), which I’m going to quote:</div>
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<div style="margin: 0px;" class="">MAKER2 was used to annotate a 10 megabase section of the C. elegans genome</div>
<div style="margin: 0px;" class="">(NGASP dataset). The algorithm was parallelized using MPI on an increasing number</div>
<div style="margin: 0px;" class="">of CPU cores. The results demonstrate how MAKER2 scales almost linearly with</div>
<div style="margin: 0px;" class="">CPU number (with a slope of near 1). If we project our results forward to the entire C.</div>
<div style="margin: 0px;" class="">elegans genome (~100 megabases), MAKER2 should take under 10 hours on 32</div>
<div style="margin: 0px;" class="">CPUs to complete; similarly, the human genome (~3 gigabases) would require fewer</div>
<div style="margin: 0px;" class="">than 24 hours on 400 CPUs</div>
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<div class="">I’m also not sure what you mean by the first run taking less time than the second run. By the first run do you mean running with est2genome turned on to create models for training ab-initio predictors? In that case, I would guess that the second
run would take longer, but it should be too big of a difference. </div>
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<div class="">~Daniel</div>
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<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Mar 31, 2016, at 6:57 AM, José Mª G. Perez-Silva <<a href="mailto:ereboperezsilva@gmail.com" class="">ereboperezsilva@gmail.com</a>> wrote:</div>
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<div class="gmail_default" style="font-family:monospace,monospace">Hello,<br class="">
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<div class="gmail_default" style="font-family:monospace,monospace">We are using Maker for the first time, and we are a little concerned about the time it takes the program to finish a whole genome (2.2Gb) ab-initio annotation.<br class="">
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<div class="gmail_default" style="font-family:monospace,monospace">In a month we have nearly annotate a half of the genome (let's say around 40% of it).<br class="">
I'd like to know how much time and under which technical specifications (processors, memory, ...) does it takes to annotate a complete genome for the first time.<br class="">
The second round of annotations (in which we use the results from the first round as extra data) is faster?<br class="">
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<div class="gmail_default" style="font-family:monospace,monospace">Thank you in advance.<br class="">
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<div class="gmail_default" style="font-family:monospace,monospace;margin-left:40px">
Jose Maria G. Perez-Silva.<br class="">
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Departamento de Biologia Molecular y Bioquimica.<br class="">
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Universidad de Oviedo.<br class="">
Spain.<br class="">
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