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

[Carson Holt]

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> 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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