[mira_talk] Re: read names too long?
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 16 Mar 2012 12:32:26 +0100
Hi Christoph,
Some arguments are positional (AFAIR). Have you tried putting the arguments
-GE:not=4:mps=6 -MI:somrnl=0 after --job=denovo,genome,accurate,solexa?
You can check in the beginning of the log file to see if the argument was
parsed correctly.
BTW, posting the exact error message, the environment you work, which version
of MIRA you use generally speeds up problem solving ;)
Cheers,
Lionel
On 16 Mar 2012, at 12:24 , Christoph Hahn wrote:
> Hello,
>
> I am trying to do denovo Solexa assembly using MIRA:
>
> mira --project=teu1-denovo-PE "--noclipping -CL:pec=no" -GE:not=4:mps=6
> -MI:somrnl=0 --job=denovo,genome,accurate,solexa SOLEXA_SETTINGS
> -GE:tismin=100:tismax=650
>
> Unfortunately, MIRA stops because of the read names being longer than 40
> characters. I have seen that before so I have already included the option
> '-MI:somrnl=0' to ignore this. Also I did mapping assemblies using the same
> data and basically the same parameters before without any problems. Any idea?
> Bug?
>
> Much obliged,
> Christoph
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