[mira_talk] Re: Assembly

  • From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 30 Sep 2009 09:44:34 +0200

"mira: command not found." tells you that your shell was not able to execute
mira.

You should add the mira bin directory to your path variable, e.g.

export PATH="/my/path/to/mira/bin:$PATH"

and then try again.

In your latter directory listing there was a file named "mira" of size "0".
It seems to me that you have copied the ">" together with mira so you
started something like

>mira ...

on the command line?

cheers,
Sven

2009/9/30 Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>

> 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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