"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 >> > >>> >> > >> >> > >> >> > > >> > >> > >