[maker-devel] Annotation of 32Mb pseudochromosome

[Carson Holt]

You can also try installing RepeatMasker with rmblast as the default aligner or hmmer as the default. That will alter it’s behavior.

Also make sure you are using blast+ version 2.2.28.  Do not use blast+ version 2.2.29

—Carson
 


> On Jul 27, 2015, at 10:15 AM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Felix, I think that idea bout the chunk sounds plausible, depending on how much of the sequence for that pseudo chromosome is N’s. Is there an error message besides the DIED for that pseudochromosome? 
> 
> ~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 Jul 27, 2015, at 7:46 AM, Felix Bemm <felix.bemm at uni-wuerzburg.de> wrote:
>> 
>> Hi,
>> 
>> I am trying to annotate a finished genome (122Mb) and maker loops forever over one of its pseudo chromosomes (32Mb). One of the child processes for that chromosomes dies with
>> 
>> DIED    RANK    13:4:0:83
>> DIED    COUNT   1
>> 
>> The rb.out file contains: RepeatMasker quit because the file pseudochr_Chr1.82.arabidopsis.rb only contains ambiguous bases, if any.
>> 
>> The assembly contains about 1,997,703 N's. Could it be that maker accidentally creates a 200kb chunk that is completely of N's and than crashes during repeat annotation? What about setting max_dna_len to something lik 25000000 and than try again?
>> 
>> Cheers,
>> Felix
>> 
>> -- 
>> University of Würzburg, Department Bioinformatics
>> Group Evolutionary Computational Biology
>> Biocentre, 97074 Würzburg, Germany
>> 
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