[mira_talk] Re: Assembly

  • From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 2 Oct 2009 14:29:54 +0530

Sorry Lionel,

Things are not working still for me, giving me the same result.

Please if you can find any other reason over the same?

Thanks and regards,
Sharmistha



On Fri, Oct 2, 2009 at 2:13 PM, Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx
> wrote:

> Thanks !! I will try as you said,
>
>
>  mira --project=cotton --job=mapping,genome,accurate,solexa -AS:nop=1
> -SB:lsd=yes:bsn=cotton_ref:bft=gbf:bbq=30 >&log_assembly.txt
>
> this was the comment I gave!!
>
> anyclue over this please let me know.
>
>
> Thanks and Regards,
> Sharmistha
>
>
>
>
>
>
> On Fri, Oct 2, 2009 at 1:47 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
>
>> Hi Sharmista,
>>
>> At least mira runs now!
>>
>> First, as far as I know, the Cotton_backbone_in.gbf file is a folder in
>> your system, whereas you should have a normal file (where did you read it
>> should be a folder containing the gbf file?). Maybe the real file is located
>> inside that folder? Thus move the gbf file into the main directory (where
>> the other input files are located)
>>
>> Second, the file names are case-sensitive, so you must have a file called
>> "cotton_backbone_in.gbf", not "Cotton_backbone_in.gbf" (note the capital C).
>>
>> Could you please paste the command you entered?
>>
>> Hope this helps,
>>
>> Lionel
>>
>>
>>
>> On 2 Oct 2009, at 9:57 , Sharmista Saha wrote:
>>
>>  Hi everyone,
>>> Now that I have reinstalled mira and reloaded the data in the bin
>>> directory of mira, now I can run mira, with your guidance. still mira = 0
>>> bytes, and log file shows
>>>
>>> AS_readpool: 0 reads.
>>> AS_contigs: 0 contigs.
>>> AS_bbcontigs: 0 contigs.
>>> Mem used for reads: 60 (60 B)
>>> and
>>> Warning: "cotton_backbone_in.gbf"
>>> : File not found.
>>> ->Thrown: GBF::load(const string & gbfin)
>>> ->Caught: main
>>>
>>> why this conclusion, when I already downloaded the respective gb file of
>>> the cotton data, renamed as .gbf and stored it in the gbf directory as
>>> directed in the manual.  Although ls -l shows me
>>>
>>> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 13:15
>>> Cotton_backbone_in.gbf
>>> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 13:15
>>> cotton_d_info
>>> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 13:15
>>> cotton_d_log
>>> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 13:15
>>> cotton_d_results
>>> -rw-r--r-- 1 sharmistha sharmistha 243851317 2009-09-16 11:03
>>> cotton.fasta
>>> -rw-r--r-- 1 sharmistha sharmistha 386595241 2009-09-16 10:56
>>> cotton.fastq
>>> -rw-r--r-- 1 sharmistha sharmistha 132828265 2009-09-19 12:58
>>> cotton_straindata_in.txt
>>> -rw-r--r-- 1 sharmistha sharmistha     22289 2009-10-02 13:15
>>> log_assembly.txt
>>> -rw-r--r-- 1 sharmistha sharmistha         0 2009-09-24 11:34 mira
>>>
>>> but, the respective directory with 4096 bytes, actually contains nothing
>>> inside it leaving the gbf directory . Mira actually is not running properly
>>> is my conclusion, I also feel it is not able to read through my ref file, so
>>> it cannot draw the respective contigs. If so, what is the reason for it? By
>>> chance if I am wrong, If the flaw lies elsewhere, please can you guide where
>>> the error actually lies?
>>>
>>> Waiting for some interesting replies
>>>
>>> Thanks and Regards,
>>>
>>> Sharmistha
>>>
>>> On Thu, Oct 1, 2009 at 10:46 AM, Sharmista Saha <
>>> sharmistasaha@xxxxxxxxxxxxxx> wrote:
>>> Thanks a lot  to both Peter and Bjorn.
>>>
>>> Regards,
>>> Sharmistha
>>>
>>>
>>> On Wed, Sep 30, 2009 at 10:00 PM, Bjoern Usadel <
>>> usadel@xxxxxxxxxxxxxxxxx> wrote:
>>> Dear Sharmista,
>>>
>>> The best bet would probably to contact the relevant  PI for the Gossypium
>>> projects: It seems finished but not yet released.
>>>
>>> http://www.jgi.doe.gov/sequencing/statusreporter/psr.php?projectid=16065
>>>
>>>
>>> Cheers,
>>> Björn
>>>
>>>
>>> Peter wrote:
>>> On Wed, Sep 30, 2009 at 4:11 PM, Sharmista Saha
>>> <sharmistasaha@xxxxxxxxxxxxxx> wrote:
>>>
>>> Hi,
>>>
>>> @Peter, thank you, for your suggestion, even myself tried with that
>>> earlier,
>>> but I do not find Gossypium, where can i get that gb file of the same?
>>>
>>>
>>> You just asked for Arabidopsis thaliana - not cotton ;)
>>>
>>> I tried searching the genomes at the NCBI with Entrez for Gossypium,
>>> but just found two chloroplasts:
>>>
>>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&term=Gossypium[orgn]
>>>
>>> I am not a plant geneticist, so I have no idea if the whole genome has
>>> been sequenced, and if it has, where else to look for it.
>>>
>>> Peter
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------
>>> Björn Usadel, PhD
>>> Max Planck Institute of Molecular Plant Physiology
>>> AG Integrative Carbon Biology
>>> Am Muehlenberg 1
>>> 14476 Potsdam-Golm
>>> Tel.: +49 331 5678153
>>> email usadel@xxxxxxxxxxxxxxxxx
>>> http://tinyurl.com/IntegrativeCarbonBiology
>>> --------------------------------------------------
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>>
>> ============================================
>> Lionel Guy
>> Thunmansgatan 25, SE-75421 Uppsala
>>
>> phone: +46 (0)18 245596
>> mobile: +46 (0)73 9760618
>> email: guy.lionel@xxxxxxxxx
>> ============================================
>>
>>
>>
>> --
>> 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
>>
>
>

Other related posts: