[mira_talk] Re: Assembly

  • From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 2 Oct 2009 15:56:00 +0530

The error in the log file:

Fatal Error: "cotton_in.solexa.fasta"
: File not found.
->Thrown: void ReadPool::loadDataFromFASTA(const string & filename, const
string & qualfilename, const bool generatefilenames, const uint8 seqtype,
const uint8 loadaction)
->Caught: Assembly::loadFASTA(const string & fastafile, const string &
fastaqualfile, const uint8 readtype, const uint8 loadaction)
Program aborted.
CWD:
/home/sharmistha/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform

Thanks and regards,
Sharmistha

On Fri, Oct 2, 2009 at 3:51 PM, Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx
> wrote:

> Hi Lionel,
>
> After following you, this is what I got.
>
> Aborted
> sharmistha@PLEX-1:~/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform$
> ls -l
> total 746468
> -rw-r--r-- 1 sharmistha sharmistha    293208 2009-10-01 10:44
> cotton_backbone_in.gbf
> 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 15:49 cotton_d_info
> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 15:49 cotton_d_log
> drwxr-xr-x 2 sharmistha sharmistha      4096 2009-10-02 15:49
> 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     18365 2009-10-02 15:49
> log_assembly.txt
> -rw-r--r-- 1 sharmistha sharmistha         0 2009-09-24 11:34 mira
>
> Now can you tell me the issue.
>
> Thanks and regards,
> Sharmistha
>
>
> On Fri, Oct 2, 2009 at 2:40 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
>
>> Rename gossypium.gbf to cotton_backbone_in.gbf:
>>
>> mv gossypium.gbf cotton_backbone_in.gbf
>>
>> and try again. If this doesn't work, send again the folder content and the
>> error message (in log_assembly.txt)
>>
>> L.
>>
>> On 2 Oct 2009, at 11:07 , Sharmista Saha wrote:
>>
>> /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
>>> ============================================
>>>
>>>
>>> --
>>> You have received this mail because you are subscribed to the mira_talk
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>>> 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
>>
>
>

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