Re: [wgs-assembler-users] resuming runCA after stop

[Walenz, B. <bw...@jc...>]

Hi, Christoph-

In general (but with exceptions) you can delete a stage and runCA will pick up from there.  For example, you can delete 4-unitigger, fiddle with parameters, and restart exactly at creating unitigs.

This works fine with overlaps.  Just delete 0-overlaptrim-overlap (and nothing else!), change parameters and restart runCA.  It will skip gatekeeper, meryl, any trimming, and move straight to configuring overlaps.

Tip:  For overlaps on large assemblies, I like to set “useGrid=1 scriptOnGrid=0”.  This will configure the overlap jobs, then print out a qsub command to run them on SGE, but not actually submit them.  I then run several jobs by hand to see memory size and compute performance.  To run by hand, in 0-overlaptrim-overlap, run “overlap.sh 1”, “overlap.sh 2” etc.  If you stop these early, they will leave an incomplete “*.WORKING.gz” file in the output directory (001/ 002/ 003/ etc).  I don’t think overlap.sh checks for these files, so you don’t even have to remove them before submitting the full batch.

b


On 4/11/12 5:02 PM, "Christoph Hahn" <chr...@gm...> wrote:

  Dear CA developers and users,

 I am trying to use Celeara assembler 7.0 to assemble a medium sized genome (about 100 Mb) using a combination of 454 and illumina reads.

 I choose a bad combination of the ovlHashBits, ovlHashBlockLength and ovlThreads options so that my last run stopped at the cluster I am using due to exceeding memory limit in the overlaptrim step. I think I know what the problem was, now, so my question is if it is possible to resume runCA from any given stage. In my particular case I would like to resume from the 0-overlaptrim-overlap stage with altered ovlHashBits, ovlHashBlockLength and ovlThreads options. I want to avaid doing the mercouts and initialtrim steps again, because they seem to have worked fine.

 I read in the manual about using the do* option to get a kind of startBefore effect. I cant seem to find any more details on this in the manual, so can you maybe help me out or point me to the required information on the webpage. Thanks!

 Your help is highly appreciated!

 much obliged,
 Christoph Hahn
 PhD student
 University of Oslo