[mira_talk] Re: Saving a crashed assembly
- From: lshen@xxxxxxxxxxx
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 10 Jul 2009 11:57:39 -0400
Hi Bastien,
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!
Lei Shen
Bastien Chevreux <bach@xxxxxxxxxxxx>
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06/17/2009 04:38 PM
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[mira_talk] Re: Saving a crashed assembly
On Mittwoch 17 Juni 2009 Jan van Haarst wrote:
> I have an assembly that got killed.
Yikes ... let me guess: a eukaryote?
> Is there a way to not have to start from the start ?
No, sorry, there is no way to restart the assembly when it went down. I've
had
only very few requests for that and implementing this feature is actually
somewhat down on the priority list. Sorry again.
Depending on when it crashed, there may be intermediate results that you
can
re-use though. Your assembly was killed at a stage where the CAF file for
a
given pass is present in it's entirety in the log directory (if
"-OUT:otc=yes"
is used, which is currently standard for I think all --job combinations of
MIRA).
If you were killed after, e.g., pass 4 of 5, then the result for pass 4
shouzld already be pretty good and you could think to use that. Look for
"SRMc" tags in the file. If only very few are present, then most repeats
will
have been resolved and you can think of using that file as result.
You could also re-launch MIRA with the temporary CAF as input file (then
reducing the number of passes accordingly), though I think I remember that
this is advisable only for bacterial projects because eukaryotes with thir
repeats may cause even longer running time than before.
> The last messages were:
> Localtime: Wed Jun 10 13:01:05 2009
>[ ...]
> It started at
> Localtime: Sat May 30 22:20:10 2009
> You can imagine that I'm not looking forward to start from the start ...
I can, indeed.
If everything fails: relaunch the assembly with -SK:mnr=yes:nrr=15 ...
this
should keep out the very worst repeats from the assembly and go pretty
quick.
Actually I'm thinking of putting this as standard for "--highlyrepetitive"
Hope this helps, please keep me informed if something does not work out as
expected.
Regards,
Bastien
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