[mira_talk] Re: condensed log file
- From: Marcus Claesson <mclaesson@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 02 Mar 2012 09:28:17 +0000
> > Is there a way to make the logs for a mira run (streamed to STDOUT) more
> > condensed and meaningful? The current default setting often produces
> > gigabytes of text without giving meaningful information to the average
>
>
> Gigabytes? That is not the usual size.
> Which version of MIRA? And is it the binary from SourceForge or compiled
> yourself? (if the latter, with which flags)
I ran a Sourceforge binary of mira-3.4.0.1 with these parameters:
--project=hybrid --job=denovo,genome,accurate,454,solexa -GE:not=6
-OUT:orm=no:org=no:ora=no
This produced a 1.5GB log file that you can access here if you want
http://biosc-sub2-169.ucc.ie/temp/log.zip
I had another case with an even bigger log file due to solexa file names being
too long.
I now know how to avoid that using -MI:somrnl=0 but there was an error message
for every solexa read...
> > non-developing user on the overall assembly progress. Many processes are
> > iterative and it's not clear at what stage the assembly is in and how
> > many more steps are left.
>
> At least the latter is quite easy:
>
> tail -f log_assembly.txt | grep ^Pass
Thanks for the advice, although I do think it would be useful with a
mira flag for condensing the log output.
Thanks,
Marcus
--
Marcus Claesson, Ph.D.
Department of Microbiology &
Alimentary Pharmabiotic Centre,
BioScience Institute,
National University of Ireland, Cork,
Western Road, Cork, Ireland
Tel: +353-(0)21-4901306
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