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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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