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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Rebecca, If you're looking at the master_datastore_index.log, then you're looking for lines with the "FINISHED" status. If you do a count on those (with "grep -c" for example),
that will tell you how many contigs have finished.
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<div>If you have 200,000,000 contigs that you're trying to annotate, you might also consider settinng the "min_contig" parameter in the maker_opts.ctl file. This parameter sets a minimum length for a contig before MAKER tries to annotate it. Usually 5000 bp
or larger is what you want. That will save you some time in the long run. </div>
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<div>Thanks,</div>
<div>Daniel<br>
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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div id="divRpF809087" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel [maker-devel-bounces@yandell-lab.org] on behalf of Rebecca Harris [rebzi87@gmail.com]<br>
<b>Sent:</b> Tuesday, February 04, 2014 3:29 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] maker output<br>
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<div dir="ltr">Hi,
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<div>I'm running maker on a cluster and am having some problems with the run ending prematurely. I would like to know if there is a straightforward way to figure out whether maker has completed. I've tried: 1) counting the number of run.log files in the datastore
directly, and 2) counting the instances of "FINISHED" in the master_datastore_index.log. These numbers are inconsistent. I have 200,000 contigs in my fasta file - do I expect 200,000 run.log files? I've had to restart maker a few times - it appears that maker
is appending to the master_datastore_index.log, as I find multiple instances of the same contig being finished. </div>
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<div>Thanks!</div>
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<div>Cheers,</div>
<div>Rebecca</div>
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