[wgs-assembler-users] CA 8.0 on large genome using PacBio

[<mic...@ip...>]

Dear WGS developers

I am trying to assemble a subset of 2 Gbp error corrected PacBio reads with CA8.0 using SGE to get a feeling about speed and  resources needed for the assembly. The full dataset will be about 13,8 Gbp of error-corrected PacBio reads. 
Read lengths range from 790 up to 19'000 bp. 
I assume its curcial to have optimal parameter settings in the spec-file. Unfortunately, i cant find appropriate examples for my dataset.  

Currently i am stuck with an error in the obt store generation: 
Failure message:

failed to build the obt store

Would it be possible provide a PacBio spec template and give me some hint about how to overcome the obt store failure? 
Attached are error-files from the runCA.sge.out , the std.err and the obtStore.err along with the used spec file. 

Thank you very much, 
Michel




________________________________________
Von: wgs...@li... [wgs...@li...]
Gesendet: Mittwoch, 13. November 2013 16:31
An: Moser, Michel (IPS)
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