[mira_talk] Re: Mira says "killed" as last word after being almost done
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 May 2011 11:12:54 -0400
Alright but investigating what you said about someone killing it i can
conclude:
- I did not do it since i was home and connected remotly to find out it is
dead
- I am the only one who has root or user access
- That means that only the OS could of killed because of exceeded resource
usage or max run time, which it is I have no idea:(
I understand what you mean about the output, I will do > next time.
Do you know anything about OS killing procs that run too much or use too
much resources?
I am not an expert, just a medium fedora user and never encountered
something like that.
Adrian
On Thu, May 12, 2011 at 11:07 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
> I'm not a bash (provided that you use bash and not csh) expert, but
> redirecting your output with ">&" sounds unusual... I just tried with
> another program, and it seems that if you do so, the output will be written
> only at the end of the run. If the program finishes it's fine, but if if
> gets killed, you won't have anything in your log file.
>
> I'd try
>
> mira --fastq --project=gigaspora -proout=gigaspora_denovo
> --job=denovo,genome,accurate,454,solexa SOLEXA_SETTINGS
> -GE:tismin=50:tismax=350;tpbd=1 > log_hybdn.txt
>
> Lionel
>
> On 12 May 2011, at 16:56 , Adrian Pelin wrote:
>
> > I have checked, no such log file was produced. MIRA was called with the
> following command:
> >
> > mira --fastq --project=gigaspora -proout=gigaspora_denovo
> --job=denovo,genome,accurate,
> > 454,solexa SOLEXA_SETTINGS -GE:tismin=50:tismax=350;tpbd=1 >&
> log_hybdn.txt
> >
> > log_hybdn.txt is an empty file 0 bytes.
> >
>
>
>
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