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

[Lassance, Jean-Marc]

Let me clarify one thing: the first pass was performed with Maker running repeatMasker internally, which is why I decided to use them in the second pass, as well as the data from the independent run of RepeatMasker.

From reading earlier posts, I gathered that Maker would use first the evidence from the rm_gff, and then from maker_gff if rm_pass=1 is activated, but that having both would not hurt. Correct?


JM



On Aug 30, 2016, at 4:12 PM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

Also make sure you pass the data in using rm_gff and not maker_gff if the repeats were not MAKER generated.

—Carson


On Aug 30, 2016, at 10:16 AM, Daniel Ence <dence at genetics.utah.edu<mailto:dence at genetics.utah.edu>> wrote:

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?

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?

Thanks,
Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Aug 30, 2016, at 7:19 AM, Lassance, Jean-Marc <lassance at fas.harvard.edu<mailto:lassance at fas.harvard.edu>> wrote:

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

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——————————————————
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

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