Re: [wgs-assembler-users] Long time for PacBiocorrection

[Francois S. <fra...@ir...>]

The script still continues to generate correction steps...

Here are the asm.layout.err for run 25 and the output of run24

Francois

PS: I changed the -t value

On 25/09/2013 18:17, Serge Koren wrote:
> Hi,
> 
> There is only one step in runCorrection.sh. If you are using CA 7.0,
> there is a known bug in the code that causes it to fail. The wiki
> documents a workaround:
> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
> 
> Re-launching the script will restart the step from the beginning. The
> output of the step is in asm.layout.err. If you can share this, it might
> give more information on how far the step is and why it may be failing.
> 
> Sergey
> 
> On Sep 23, 2013, at 5:22 AM, Francois Sabot <fra...@ir...
> <mailto:fra...@ir...>> wrote:
> 
>> Hi folks
>>
>> I am running the PacBioToCa on my entire set of data (coverage 12x
>> PacBio, 55x Illumina, genome size ~ 400-450 Mb).
>>
>> I have few weird errors of missed linked, and i re-launch regularly the
>> script to ensure its completion.
>>
>> My question s how can you calculate the numbers of steps in the
>> runCorrection.sh part ? It is already on the 19th one, and it ran for
>> days....
>>
>> Can someone help me ?
>>
>> Francois
>>
>> -- 
>> --------------------------------------------------------
>> Francois Sabot, PhD
>>
>> Be realistic. Demand the Impossible.
>> http://bioinfo.mpl.ird.fr/
>> http://www.mpl.ird.fr/rice
>> -----------------------------------------
>> UMR DIversity, Adaptation & DEvelopment
>> Centre IRD
>> 911, Av Agropolis BP 64501
>> 34394 Montpellier Cedex 5
>> France
>> Phone: +33 4 67 41 64 18
>> -----------------------------------------
>>
>> ------------------------------------------------------------------------------
>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8,
>> SharePoint
>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack
>> includes
>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
>> wgs-assembler-users mailing list
>> wgs...@li...
>> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
> 

-- 
--------------------------------------------------------
Francois Sabot, PhD

Be realistic. Demand the Impossible.
http://bioinfo.mpl.ird.fr/
http://www.mpl.ird.fr/rice
-----------------------------------------
UMR DIversity, Adaptation & DEvelopment
Centre IRD
911, Av Agropolis BP 64501
34394 Montpellier Cedex 5
France
Phone: +33 4 67 41 64 18
-----------------------------------------