[maker-devel] annotation of birch genome

[Jasmin Zohren]

Dear Maker developers,

 

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.

 

My current project is about birch which has just been sequenced and I now
want to annotate it. Here are the details:

 

-          Genome size: 560 Mb

-          Size of EST file (from a related species): 28 Mb

-          I am running it on a single node with 20 cores of 512 GB RAM
(using "mpiexec -n 20 maker")

 

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.

 

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.

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.

 

Many thanks in advance and kind regards,

Jasmin

 

-----------------------------

Jasmin Zohren

PhD student in the INTERCROSSING ITN

Queen Mary University of London

 

intercrossing.wikispaces.com <http://intercrossing.wikispaces.com/> 

evolve.sbcs.qmul.ac.uk <http://evolve.sbcs.qmul.ac.uk/buggs/jasmin-zohren/> 

 

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