[mira_talk] Re: Assembly
- From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 30 Sep 2009 13:04:51 +0530
Thanks for the quick response.
ans: 1. I do have all the respective files in the folder I am running mira.
2. They do all have the correct names. Eg: mydata.fasta; mydata.fastq;
mydata_backbone_in.gbf; mydata_straindata_in.txt, my seq.gbf
3. I ran the respective command you provided, unfortunately, error says:
bash: mira: command not found.
Now can it be easier for you to guide me to the root of my errors?
Please I am waiting.
Thanks and Regards,
Sharmistha
On Wed, Sep 30, 2009 at 12:40 PM, Davide Sassera (davide.sassera) <
davide.sassera@xxxxxxxx> wrote:
> 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
> > >>>
> > >>>
> > >>> --
> > >>> You have received this mail because you are subscribed to
> > the mira_talk
> > >>> mailing list. For information on how to subscribe or
> > unsubscribe, please
> > >>> visit http://www.chevreux.org/mira_mailinglists.html
> > >>>
> > >>
> > >>
> > >
> >
>
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