[mira_talk] Re: reconstructing results from crashed MIRA
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 19 Aug 2009 03:39:13 -0700
I'm sure I'll be corrected if I'm wrong but i think you may be out of luck.
I have pasted Basteins answer to a similar problem below. Hope this helps
until you get a better, more knowledgeable reply
regards
Brian
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."
On Wed, Aug 19, 2009 at 3:25 AM, Burkhard Steuernagel <
steuerna@xxxxxxxxxxxxxxxxxx> wrote:
> Hi all,
> I have a problem and hope you can help me.
> I had MIRA running for about two weeks. Then my server crashed (I think
> this had nothing to do with MIRA) and the run was not finished. I believe
> that MIRA was right before finishing because parts of the result files are
> already written. So my question is: Is there a chance to reconstruct the
> result from the files in the log dir?
> Thanks
> Burkhard
>
>
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"If scientists knew what they were doing they wouldn't call it research"
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