[wgs-assembler-users] Spec file setup and long run time issues

[Seth M. <mu...@uw...>]

Hello Everyone,

I'm new to CA and I'm trying to use 8.3 to correct some PacBio reads.
Installation went smoothly, but when it comes time to run I first hit the
problem of a missing spec file.  After some googling I found an example
posted on the seqanswers forums (
http://seqanswers.com/forums/archive/index.php/t-18478.html), however it's
for Celera 7.  I went through and compared the spec options to the options
parameters that print at the start of the PBcR run and removed everything
except the memory related entries.  I wanted to see what the default values
gave me before I tried tweaking things, but I have more memory available to
me and I presumed the command line -threads option did the same thing as
altering the spec values concerning threads.

My spec file consisted of the following:
assemble = 0
ovlMemory = 250
merylMemory = 256000
ovlStoreMemory = 256000

The command I ran it with was:
PBcR -threads 30 -libraryname PI440795_A08 -s PI440795.spec -fastq
PI440795_A08.fastq Pacu1.frg Pacu2.frg

Once I try to run it, however, I realize I've done something wrong.  The
PBcR run has been on OverlapInCore for hours at this point and is using
~5GB of RAM.

The second problem I faced came when I tried using a smaller dataset to see
if it was a size based issue and it moved through that stage within a day,
and moved beyond the correction, but then it stalled on runPartition.sh,
using ~10GB of RAM and taking ~1.5 hours per partition, while showing
essentially no CPU usage.

I've since come across the RunCA wiki page which outlines many of the spec
options, and found that many the options I started with from the example
spec file don't even exist anymore.  Would anyone be able and willing to
lend me a hand so I can properly configure my Celera pipeline to correct my
PacBio reads please?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755