[mira_talk] Re: Assembly

Dear Sharmista,

1: do you have all the necessary files in the folder you are running mira?

2: do they have all the correct names? please provide a list of the files

3: I think The command should be:

mira -project=my_project -job=mapping,genome,accurate,solexa -AS:nop=1 
-SB:lsd=yes:bsn=myproject_ref:bft=gbf:bbq=30

Ciao
D.


----- Messaggio Originale -----
Da: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
Data: Mercoledi', Settembre 30, 2009 8:58 am
Oggetto: [mira_talk] Re: Assembly
A: mira_talk@xxxxxxxxxxxxx

> The command I typed was as follows:
> sharmistha@PLEX-
> 1:~/Sharmistha/Bioinfo/Project_data/my_project/mira/Dataform>mira
>  --project=my_project --job=mapping,genome,accurate,solexa* 
> *-AS:nop=1
> 
> *  -SB:lsd=yes:bsn=myproject_ref:bft=gbf:bbq=30
>   >&log_assembly.txt }
> 
> 
> 
> *This was my comand line..........
> 
> now can you suggest me, where am I wrong?
> 
> Thanks and Regards,
> 
> Sharmistha
> 
> 
> 
> On Wed, Sep 30, 2009 at 12:14 PM, Sven Klages
> <sir.svencelot@xxxxxxxxxxxxxx>wrote:
> 
> > You still didn't provide the command you typed in. So it's 
> difficult to
> > tell what went wrong.
> >
> > cheers,
> > Sven
> >
> > 2009/9/30 Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
> >
> > Can anyone solve my required issue? I need it very much and am 
> very curious
> >> to see  how my denovo assembly happens via mira,. 
> Please, if anyone can
> >> direct me my error in execution of mira, I shall be highly 
> grateful.  I am
> >> still positive about the tool to work in my sequence too, 
> when it can
> >> resolve so many queer issues.
> >>
> >> Only my sequence is  a solexa sequence.  waiting 
> hopefully for some
> >> positive response on the same ground.
> >>
> >> Thanks and Regards,
> >> Sharmistha
> >>
> >>
> >> On Fri, Sep 25, 2009 at 2:06 AM, Bastien Chevreux 
> <bach@xxxxxxxxxxxx>wrote:>>
> >>> On Donnerstag 24 September 2009 Sharmista Saha wrote:
> >>> > [...]
> >>> > This is what I got. Hope this answers your query.
> >>>
> >>> Not entirely, you forgot the command line you typed in. 
> Fortunately, the
> >>> directory listing you provided gives a hint to what happened.
> >>>
> >>> Do NOT type the command line prompt that is shown in the 
> examples, it's
> >>> NOT
> >>> part of the mira command!
> >>>
> >>> Hope that helps.
> >>>
> >>> Regards,
> >>>  Bastien
> >>>
> >>>
> >>> --
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> >>>
> >>
> >>
> >
>

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