Re: [wgs-assembler-users] runCA stopped while updating overlapStore - how to resume???

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hi Christoph.

This is not an answer to your question, but a suggestion for a
work-around. If I remember correctly, you have both Illumina and 454
reads. Celera runs, as you see below, frgcorrection and overlap based
trimming to correct 454 reads, and merTrim to correct Illumina reads
(can also be used on 454 reads). What I've been doing lately, is to
run meryl on a trusted set of Illumina reads, pair end for example, I
ran it on some overlapping reads which I had merged with FLASH. Then
you can use the set of trusted k-mers to correct different datasets.
For example, I first ran CA to the end of OBT (overlap based trimming)
for my 454 reads, and then output the result as fastq-files. I used
the trusted k-mer set to correct these 454 reads too. If you do this
for all your reads, used either merTim or merTrim/OBT, and do
deduplication on all the datasets too, then you'll end up with reads
that you can use in assemblies where you skip relatively expensive
steps as frgcorrection.

I don't think frgcorrection is that useful for the type of data you're
using anyway.

If you have a set of corrected reads, you can use these settings for CA:
doOBT=0
doFragmentCorrection=0

When I think of it, you might use doFragmentCorrection=0 on this
assembly now. You might have to clean up your directory tree, like
removing the 3-overlapcorrection directory and maybe some other steps
too. Apply with caution.

Most of the stuff I've mentioned I've taken from here:
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Preprocessing
and discussion with Brian.

Ole

On 9 July 2012 12:47, Christoph Hahn <chr...@gm...> wrote:
> Dear users and developers,
>
> I have the following problem: In my assembly process I have just completed
> the fragment- and overlap error correction. Unfortunately runCA stopped in
> the subsequent updating of the overlapStore, because of an incorrectly set
> time limit..
> If I am trying to resume the assembly now, I get the following error:
> ----------------------------------------START Mon Jul  9 11:05:53 2012
> /xanadu/home/chrishah/programmes/wgs-7.0/Linux-amd64/bin/overlapStore  -u
> /projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore
> /projects/nn9201k/Celera/work2/salaris1/3-overlapco
> rrection/salaris.erates>
> /projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/overlapStore-update-erates.err
> 2>&1
> ----------------------------------------END Mon Jul  9 11:05:54 2012 (1
> seconds)
> ERROR: Failed with signal HUP (1)
> ================================================================================
>
> runCA failed.
>
> ----------------------------------------
> Stack trace:
>
>  at /usit/titan/u1/chrishah/programmes/wgs-7.0/Linux-amd64/bin/./runCA line
> 1237
>         main::caFailure('failed to apply the overlap corrections',
> '/projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/o...') called
> at /usit/titan/u1/chrishah/programmes/wgs
> -7.0/Linux-amd64/bin/./runCA line 4077
>         main::overlapCorrection() called at
> /usit/titan/u1/chrishah/programmes/wgs-7.0/Linux-amd64/bin/./runCA line 5880
>
> ----------------------------------------
> Last few lines of the relevant log file
> (/projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/overlapStore-update-erates.err):
>
> AS_OVS_openBinaryOverlapFile()-- Failed to open
> '/projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore/0001~' for
> reading: No such file or directory
>
> ----------------------------------------
> Failure message:
>
> failed to apply the overlap corrections
>
>
>
> So it can obviously not find the file /salaris.ovlStore/0001~. The reason
> is, from what I can see, that the /salaris.ovlStore/0001~ file has already
> been updated to /salaris.ovlStore/0001 before it stopped. In fact it seems
> to have stopped after updating /salaris.ovlStore/0249 (of 430). Is there a
> way to tell runCA to continue from  /salaris.ovlStore/0250~, instead of from
> 0001~, which is obviously not there any more??
> Another solution I was thinking of is to run the previous overlapStore
> command again manually (the one that was done before starting the frgcorr
> and ovlcorr:
> /xanadu/home/chrishah/programmes/wgs-7.0/Linux-amd64/bin/overlapStore  -c
> /projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.BUILDING  -g
> /projects/nn9201k/Celera/work2/salaris1/salaris.gkpStore  -i 0 -M 14000 -L
> /projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.list  >
> /projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.err 2>&1) to
> restore the status from before the frgcorr and ovlcorr steps, before
> resuming runCA. This should restore the 0001~ file, right? The most
> important thing is that I want to avoid rerunning the frgcorr and ovlcorr
> steps, because these steps were really resource intensive.
>
> I would really appreciate any comments or suggestions to my problem! Thanks
> in advance for your help!
>
> much obliged,
> Christoph
>
> University of Oslo
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> wgs-assembler-users mailing list
> wgs...@li...
> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>