[mira_talk] Re: hybrid assembly crashes - file not found

On Friday 06 March 2009 Andreas Petzold wrote:
> I try to build a hybrid assembly with 454 and Sanger sequences and mira
> (2.9.39) crashes before the alignment phase:
>[...]
> 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 ...

Hi Andreas,

interesting error, one from the category "should not happen." Indeed, these 
files contain the hits from skim ... and both are created empty, one after the 
other, at the same time. That is: they always (should) exist, even if empty.

Which makes me wonder what could cause the symptoms you are seeing.

> 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 ...

Care to explain a bit more in detail what you tried? EXP being the first data 
format that was implemented in MIRA (even before FASTA), it should work. 
Except if the EXP files come from an existing assembly and contain edits, I 
never implemented loading this type as CAF was a far better alternative.

Regards,
  Bastien


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