[mira_talk] Re: Assembly
- From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 2 Oct 2009 13:27:28 +0530
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]<http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&term=Gossypium%5Borgn%5D>
>>>
>>> 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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>
>
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