[mira_talk] hybrid assembly crashes - file not found

Hi,

I try to build a hybrid assembly with 454 and Sanger sequences and mira 
(2.9.39) crashes before the alignment phase:

Fatal Error: "Nf_genomic_d_log/Nf_genomic_int_posmatchc_preassembly.0.lst"
: File not found?
->Thrown: uint32 Assembly::countLinesInFile(const string & filename)
->Caught: main
Program aborted.
Program aborted.
CWD: /misc/vulpix/data/andpet/Nothobranchius/genomic
CWD: /misc/vulpix/data/andpet/Nothobranchius/genomic


The missing Nf_genomic_int_posmatchc_preassembly.0.lst contains all complement 
skim hits, right ? The funny thing is that
the file for the "forward" hits, Nf_genomic_int_posmatchf_preassembly.0.lst, 
exists ...

I think I got the problem at least a little bit cornered because I tried to 
assemble 454 and sanger sequence separately and
454 worked but not Sanger.

The Sanger sequences are in EXP format and have trace data, could that be the 
problem ??? Will check this ...

Thanks a lot,

Andreas

--

Andreas Petzold
Genome Analysis
Fritz Lipmann Institute
Beutenbergstrasse 11, D-07745 Jena
voice : ++49-3641-656488
fax   : ++49-3641-656488
email : andpet@xxxxxxxxxxxxxx

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