[maker-devel] maker2.31.8 _ failure when processing repeats

[Lassance, Jean-Marc]

Hi.

I am using Maker2.31.8  to annotate a mammalian genome (with OpenMPI, Linux server).

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:

rm_gff=myanimal.repeatmasker.out.gff3

#-----Re-annotation Using MAKER Derived GFF3
maker_gff=myanimal.all.maker.pass1.gff
rm_pass=1

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:

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.
--> rank=26, hostname=holy2a11102.rc.fas.harvard.edu<http://holy2a11102.rc.fas.harvard.edu>
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:scaffold00013

I wonder if you have an idea of what could be wrong here.

Thanks for your help,


Jean-Marc

——————————————————
Jean-Marc Lassance, PhD

Harvard University
Department of Organismic and Evolutionary Biology
Department of Molecular and Cellular Biology
Museum of Comparative Zoology

26, Oxford Street
Cambridge MA 02138
USA

email: lassance at fas.harvard.edu<mailto:lassance at fas.harvard.edu>
twitter: @lassancejm

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160830/9c7ab2e9/attachment-0002.html>