[mira_talk] Re: Assembly

/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform$
ls -l
total 746472
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 14:27 cotton_d_info
drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 14:27 cotton_d_log
drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 14:27
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    293208 2009-10-01 10:44 gossypium.gbf
-rw-r--r-- 1 sharmistha sharmistha     22285 2009-10-02 14:27
log_assembly.txt
-rw-r--r-- 1 sharmistha sharmistha         0 2009-09-24 11:34 mira

I hope this will serve the purpose.

Just check out and let me know.

Thanks and regards

Sharmistha

On Fri, Oct 2, 2009 at 2:34 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:

> Can you please copy/paste your folder contents as before, along with the
> error message?
> L.
>
>
> On 2 Oct 2009, at 10:59 , Sharmista Saha wrote:
>
>  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
>> --------------------------------------------------
>>
>>
>>
>> --
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>>
>>
>> ============================================
>> Lionel Guy
>> Thunmansgatan 25, SE-75421 Uppsala
>>
>> phone: +46 (0)18 245596
>> mobile: +46 (0)73 9760618
>> email: guy.lionel@xxxxxxxxx
>> ============================================
>>
>>
>>
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>>
> ============================================
> Lionel Guy
> Thunmansgatan 25, SE-75421 Uppsala
>
> phone: +46 (0)18 245596
> mobile: +46 (0)73 9760618
> email: guy.lionel@xxxxxxxxx
> ============================================
>
>
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