[mira_talk] Re: Mira says "killed" as last word after being almost done

I run mira in one of the following ways in bash to log messages/errors:

   - *Straight to file: *mira <options> > log.file
   - *To a file and screen: *mira <options> | tee log.file
   - Same thing as above but also captures STDERR (not just STDOUT)
      - mira <options> 2>&1 > log.file
      - mira <options> 2>&1 | tee log.file


On Thu, May 12, 2011 at 8:07 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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