Re: [wgs-assembler-users] caught in overlap.sh?

[Schwartz, A. <asc...@sy...>]

I have experienced the same issue with our hybrid assemblies.
Currently I am waiting for an overlap job that has been running for almost two weeks.

I wonder if there are some recommended settings that could be used to alleviate this problem.

Thanks,

Ariel

Ariel Schwartz, Ph.D.
Senior Scientist, Bioinformatics
Synthetic Genomics, Inc.

On 4/24/12 4:44 AM, "Christoph Hahn" <chr...@gm...<mailto:chr...@gm...>> wrote:

Dear CABOG developers and users,

I am trying to do a hybrid assembly using a combination of 454 and
single- as well as paired-end illumina data.

After initial trouble with optimization in the 0-overlaptrim-overlap
stage of my assembly I got it to run succesfully and during the previous
7+ days the pipeline succesfully completetd some 2260 overlap.sh jobs.
Now I am encoutering something strange:  The last pending overlap.sh job
(2148 of 2261) is running now already for over 36 hours. The
002148.ovb.WORKING.gz file created by this job is slowly but steadily
growing. It presently has some 631 M. Is this normal? Has anyone had a
similar experience before? Maybe it will sort out it self eventually
anyway, I am just a little concerned that CABOG will not finish the job
until it hits the 10 days wall clock limit that is set on the cluster
for the job, which would result in thousands of CPU hours going down the
drain..

Please share your wisdom with me!

much obliged,
Christoph Hahn
PhD fellow
University of Oslo
Norway

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