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<p>Thanks Carson. <br>
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<p>I thought also to use only swissprot at the beginning but I am working with a non model organism and I am scared that swissprot is not enough complete to capture all the gene prediction.</p>
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<p>but if I use nr and I select only gene with AED < 0.5, it should be good no ? or do you have an AED cut off to recommend ?</p>
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<p>Cheers.<br>
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Patrick</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Thursday, January 17, 2019 10:31:17 PM<br>
<b>To:</b> Patrick Tran Van<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: Maker crash with big protein evidence ?</font>
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<div>You may be running out of RAM. You can try setting depth_blast= parameters in maker_bopts.ctl to something like 10 or 20 to throw away more redundant data. But I would also suggest not using NR. It’s not curated to the extent swiss-prot is, so you will
get a lot of poor models. The result will be a lot of bad false hints sent to the predictors (trash in trash out).
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<div class="">On Jan 15, 2019, at 2:54 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I run maker with mpi and default option.<span class="Apple-converted-space"> </span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">It works well with swissprot/uniprot as protein evidence but I wanted to provide a larger database (nr) and it run for a while but for longer scaffold it crashs after this :</div>
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<div class="">in cluster::shadow_cluster...<br class="">
sorting hits in shadow cluster...<br class="">
j_size:3 current j:0<br class="">
j_size:3 current j:1<br class="">
j_size:3 current j:2<br class="">
...finished clustering.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Did you already face something similar ?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks.<br class="">
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Patrick </div>
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