[maker-devel] Annotation of 32Mb pseudochromosome

[Felix Bemm]

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