[mira_talk] Re: Saving a crashed assembly

On Freitag 10 Juli 2009 lshen@xxxxxxxxxxx wrote:
> I have an EST assembly that got cut short during the final output stage
> because the disk ran out of space. This is an assembly that had been
> running for a month. You mentioned that you could re-launch MIRA with the
> temporary CAF file as input. I have the temporary CAF file for pass 6 so I
> would like to give it a try. Can you tell me what is the syntax for doing
> that? Thanks a lot!

Hello Lei,

hmmm ... 7 rounds for an EST assembly? Can you tell me what your command line 
was (and the version of MIRA you were using?), this seems a bit excessive to 
me. Maybe I made a configuration error on the quick switches.

Honestly, I would not try to assemble one more round, it's probably more 
hassle than it's worth. The results in the CAF file from pass 6 should be fine 
as they are. You can quickly check by looking at the file 
*_info_consensustaglist.6.txt in the log directory: if no "SROc" tag is 
present, everything should be fine. Even "a few" SROc tags won't spoil the 
results ... you might just perhaps want to have a look at the contigs 
containing them.

Just out of curiosity: how many reads (and which technology) did you run with? 
One month of calculation is too much, even for MIRA. I know I haven't 
optimised the EST assemblies as much as genome assemblies lately, so I'd be 
interested to have a look at the output log of this assembly and see whether I 
can find something to enhance.

Regards,
  Bastien

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