[mira_talk] Re: Assembly

  • From: Lionel Guy <guy.lionel@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 2 Oct 2009 12:40:30 +0200

Right... You also need to rename the following files:
cotton.fasta -> cotton_in.solexa.fasta
cotton.fastq -> cotton_in.solexa.fasta.qual

Depending on the format of your cotton.fastq file, you might run into further problems. Copied from mira_solexa manual: Note 1: mira expects the quality file to contain Solexa scores (but only one per base), not phred style quality scores. Should you have already the scores already converted to phred style, you will need to set -LR:ssiqf=no.

Note 2: Should your quality file contain negative values, you have Solexa scores. Else you probably have phred scores.

L.


On 2 Oct 2009, at 12:26 , Sharmista Saha wrote:

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



--
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Björn Usadel, PhD
Max Planck Institute of Molecular Plant Physiology
AG Integrative Carbon Biology
Am Muehlenberg 1
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Tel.: +49 331 5678153
email usadel@xxxxxxxxxxxxxxxxx
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phone: +46 (0)18 245596
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email: guy.lionel@xxxxxxxxx
============================================


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phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================


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