<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Also make sure you pass the data in using rm_gff and not maker_gff if the repeats were not MAKER generated.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 30, 2016, at 10:16 AM, Daniel Ence <<a href="mailto:dence@genetics.utah.edu" class="">dence@genetics.utah.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hi Jean-Marc, so the first question I have is whether maker is still annotating repeats, even though you’re providing the rm_gff file. Are you providing a file or parameter for repeat masker in the maker_opts.ctl file?
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<div class="">And secondly, what about the scaffold that is failing? How long is it, what is the percent N’s in the sequence there, and how much of it was masked in the rm_gff file? </div>
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<div class="">Thanks,</div>
<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 Aug 30, 2016, at 7:19 AM, Lassance, Jean-Marc <<a href="mailto:lassance@fas.harvard.edu" class="">lassance@fas.harvard.edu</a>> wrote:</div>
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<div class="">Hi. </div>
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<div class="">I am using Maker2.31.8 to annotate a mammalian genome (with OpenMPI, Linux server). </div>
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<div class="">Basically, after running Maker a first time to generate a training set for SNAP, I am running it a second time with SNAP and Augustus enabled. Because we ran RepeatMasker independently, I am providing the gff3 like so:</div>
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<div class="">rm_gff=myanimal.repeatmasker.out.gff3</div>
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<div class="">#-----Re-annotation Using MAKER Derived GFF3</div>
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<div class="">maker_gff=myanimal.all.maker.pass1.gff </div>
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<div class="">rm_pass=1</div>
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<div class="">Things seem to progress nicely (the vast majority of the scaffolds “finish”), but one of the scaffolds keeps failing (I have attempted to restart after erasing the entire content of the output folder). This is the message that I could associated
with this error:</div>
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<div class="">Died at /n/sw/fasrcsw/apps/MPI/gcc/4.8.2-fasrc01/openmpi/1.10.0-fasrc01/maker/2.31.8-fasrc01/bin/../perl/lib/Bio/Search/Hit/PhatHit/Base.pm line 188.</div>
<div class="">--> rank=26, hostname=<a href="http://holy2a11102.rc.fas.harvard.edu/" class="">holy2a11102.rc.fas.harvard.edu</a></div>
<div class="">ERROR: Failed while processing all repeats</div>
<div class="">ERROR: Chunk failed at level:3, tier_type:1</div>
<div class="">FAILED CONTIG:scaffold00013</div>
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<div class="">I wonder if you have an idea of what could be wrong here. </div>
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<div class="">Thanks for your help,</div>
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<div class="">Jean-Marc</div>
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<div class="">——————————————————<br class="">
Jean-Marc Lassance, PhD<br class="">
<br class="">
Harvard University<br class="">
Department of Organismic and Evolutionary Biology<br class="">
Department of Molecular and Cellular Biology<br class="">
Museum of Comparative Zoology<br class="">
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26, Oxford Street<br class="">
Cambridge MA 02138<br class="">
USA<br class="">
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email: <a href="mailto:lassance@fas.harvard.edu" class="">lassance@fas.harvard.edu</a><br class="">
twitter: @lassancejm </div>
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