[mira_talk] Re: Message "Failure, wrapped MIRA process aborted."
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 5 May 2014 10:43:55 +0100
On Thu, Nov 14, 2013 at 11:59 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>> On November 14, 2013 at 12:22 PM Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
>> wrote:
>> I presume from the discussion here
>> http://sourceforge.net/p/mira-assembler/tickets/6/?limit=25
>> that "Failure, wrapped MIRA process aborted." is just a way of
>> the operating system (or in this case maybe SGE) killing MIRA?
>
> Probably. The only way to know for sure is when having stderr also
> redirected to a file (or even the same file) as stdout, because the OS
> normally gives a short on-line reason there. Of course one is SOL if stderr
> was not redirected because I have no idea if it is possible to check by
> return code whether the killing was done by the OS or not.
>
> B.
>
> PS: just out of curiosity, could you send me the complete log of the failed
> run and one of its siblings which succeeded? I'd like to see whether I can
> find some heuristics which warn the user early.
I'm looking at these same group of datasets again, these are viral
samples with massive over coverage on a MiSeq.
I wanted to do a quick comparison to a know virus (one contig),
and so tried MIRA 4.0.1 in mapping mode. Again it was killed,
"Failure, wrapped MIRA process aborted." (error 100).
I tried twice, and it got further on a higher memory machine.
The MIRA manual suggests mapping mode can handle two or three
times the coverage of de novo mode (RAM limited). This dataset
clearly exceeds that - but does MIRA do a crazy coverage check
in mapping mode? My guess is not based on the following:
$ grep -i cov /mnt/galaxy/galaxy-dist/database/files/013/dataset_13116.dat
Coverage threshold (ardct) : [sxa] 2
Automatic incr. cov. threshold (bphaict): 20
Freq. cov. estim. min (fcem) : 0
Nasty repeat coverage (nrc) : 0
Check average coverage (cac) : stop
Average coverage value (acv) : 160
Measured avg. raw frequency coverage: 10
Corrected avg. raw frequency coverage: 10
Min normal cov: 4
Max normal cov: 16
Repeat cov: 19
Heavy cov: 80
Crazy cov: 200
Mask cov: 1000
Measured avg. raw frequency coverage: 10
Corrected avg. raw frequency coverage: 10
Min normal cov: 4
Max normal cov: 16
Repeat cov: 19
Heavy cov: 80
Crazy cov: 200
Mask cov: 1000
Measured avg. raw frequency coverage: 17553
Corrected avg. raw frequency coverage: 8358 SKEWED DISTRIBUTION!
Min normal cov: 3343.2
Max normal cov: 13372.8
Repeat cov: 15880.2
Heavy cov: 66864
Crazy cov: 167160
Mask cov: 835800
Timing BFC analysereadcov: 18137856
Max. coverage 0 0 0 0
0 3 31831 0
Avg. coverage 0.000 0.000 0.000 0.000
0.000 1.000 3569.744 0.000
Max. contig coverage: 31834
Avg. contig coverage: 3570.744
Contig positions with coverage: 0
Clearly naively feeding this raw data into MIRA is appropriate, but
the downside of making a nice Galaxy wrapper is that is very easy
to do. I'll look at a more traditional read mapper for this, and/or
sampling.
Regards,
Peter
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