[mira_talk] Re: Saving a crashed assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 13 Jul 2009 22:29:18 +0200
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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