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

[Serge K. <se...@um...>]

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...> 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
> 
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