Re: [wgs-assembler-users] CA on BlueGene server at Rice University

[Elton V. <elt...@iq...>]

Hy Brian and Serge,

I forgot to tell you last week that I am not doing PacBio reads
self-correction. Instead I'm doing hybrid assembly (26 SMRTcells plus 3
paired-end Illumina libraries).
### Question 1: ###
Is it still worthwhile doing that in a single multi-thread machine?
Cause I've seen a Sergey's comment that the pipeline is quite slower when
considering correction with Illumina reads (
http://ehc.ac/p/wgs-assembler/mailman/message/33620582/)

I am now running CA on a sinlge multi-thread server that has 80 threads and
1T RAM.
It spent about 5 days on the "overlapInCore" step and I had to kill the
process because of server owner's complaint about too many threads being
consumed for a long time period.

### Question 2: ###
Could you explain me why "overlapInCore" is using all available threads
(80) instead of only the user's request (20)?
My spec file is attached and I ran the following command:
$ nohup /home/elton/wgs-8.3rc2/Linux-amd64/bin/pacBioToCA -l Test01
-threads 20 -shortReads -genomeSize 380000000 -s pacbio.spec -fastq
26-SMRTcells-filtered_subreads.fastq illumina-NEW.frg  &

Thanks a lot again for your attention and support,
Best,
Elton


2015-06-03 11:43 GMT-03:00 Serge Koren <ser...@gm...>:

> Yes, the latest CA 8.3 release can assemble D. melanogaster in < 700CPU
> hours. You can see the updated timings here:
>
> http://wgs-assembler.sourceforge.net/wiki/index.php/Version_8.3_Release_Notes
>
> I’ve routinely run D. melanogaster on a 16-core, 32GB machine in less than
> a day (I haven’t timed it exactly) so for your genome you’re looking at
> 3-4K cpu hours. You should be able to run it on a single 16-core 32GB
> machine in a couple of days so I think it’s easiest to run it on a single
> largish machine you have access to.
>
> Sergey
>
> On Jun 2, 2015, at 9:12 PM, Brian Walenz <th...@gm...> wrote:
>
> That's an old page.  The most recent page, linked from
> http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page, is:
>
> http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
>
> (look for 'self correction')
>
> I've run drosophilia on my 12-core development machine in a few hours to
> overnight (I haven't timed it).  Sergey replaced blasr with a much much
> faster algorithm, and that was where most of the time was spent.
>
> b
>
>
> On Tue, Jun 2, 2015 at 9:02 PM, Elton Vasconcelos <elt...@iq...>
> wrote:
>
>> Thanks for the hints, Brian!
>>
>> We'll try everything you suggested tomorrow, back in the lab.
>> Then I'll tell you what we got.
>> For now, I only wanna say that our main concern, instead of running runCA
>> itself, is gonna be with the pre-assembly (correction) step, running
>> PacBiotoCA and PBcR pipeline that are embedded in the wgs package.
>> Please take a look at the following strategy to assemble the Drosophila
>> genome sequenced by PacBio technology (which presents a high error rate on
>> the base calling, ~15%)  at CBCB in Maryland :
>> http://cbcb.umd.edu/software/PBcR/dmel.html
>> They mentioned 621K CPU hours to correct that genome of ~122 Mb.
>> Our organism genome is something like 380 Mb long. Three times
>> Drosophila's one.
>> Well, just to let you know again! ;-)
>>
>> Talk to you later,
>> Thanks again.
>> Good night!
>> Elton
>>
>> 2015-06-02 20:19 GMT-03:00 Brian Walenz <th...@gm...>:
>>
>>> For the link problems - all those symbols come out of the kmer package.
>>> Check that the flags and compilers and whatnot are compatible with those in
>>> wgs-assembler.
>>>
>>> The kmer configuration is a bit awkward.  A shell script (configure.sh)
>>> dumps a config to Make.compilers, which is read by the main Makefile.
>>> 'gmake real-clean' will remove the previous build AND the Make.compilers
>>> file.  'gmake' by itself will first build a Make.compilers by calling
>>> configure.sh, then continue on with the build.  The proper way to modify
>>> this is:
>>>
>>> edit configure.sh
>>> gmake real-clean
>>> gmake install
>>> repeat until it works
>>>
>>> In configure.sh, there is a block of flags for Linux-amd64.  I think
>>> it'll be easy to apply the same changes made for wgs-assembler.
>>>
>>> After rebuilding kmer, the wgs-assembler build should need to just link
>>> -- in other words, remove just wgs-assembler/Linux-amd64/bin -- don't do
>>> 'gmake clean' here!  You might need to remove the dependency directory
>>> 'dep' too.
>>>
>>>
>>> For running - the assembler will emit an SGE submit command to run a
>>> single shell script on tens-to-hundreds-to-thousands of jobs.  Each job
>>> will be 8-32gb (tunable) and 1-32 cores (nothing special here: more is
>>> faster, fewer is slower).  If you can figure out how to run jobs of the
>>> form "command.sh 1", "command.sh 2", "command.sh 3", ..., "command.sh N" on
>>> on BG/Q you're most of the way to running CA.  To make it output such a
>>> submit command, supply "useGrid=1 scriptOnGrid=0" to runCA.
>>>
>>> The other half of the assembler will be either large I/O or large
>>> memory.  If you've got access to a machine with 256gb and 32 cores you
>>> should be fine.  I don't know what a minimum usable machine size would be.
>>>
>>> So, the flow of the computer will be:
>>>
>>> On the 256gb machine:  runCA useGrid=1 scriptOnGrid=0 ....
>>> Wait for it to emit a submit command
>>> Launch those jobs on BG/Q
>>> Wait for those to finish
>>> Relaunch runCA on the 256gb machine.  It'll check that the job outputs
>>> are complete, and continue processing, probably emitting another submit
>>> command, so repeat.
>>>
>>> Historical note: back when runCA was first developed, we had a DEC Alpha
>>> Tru64 machine with 4 CPUs and 32gb of RAM, and a grid of a few hundred 2
>>> CPU, 2gb, 32-bit Linux machines.  The Alpha wasn't in the grid, and a
>>> different architecture anyway, so we had to run CA this way.  It was a real
>>> chore.  We're all spoiled with our 4 core 8gb laptops now...
>>>
>>> b
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Jun 2, 2015 at 5:49 PM, Elton Vasconcelos <elt...@iq...>
>>> wrote:
>>>
>>>> Thanks Brian, Serge and Huang,
>>>>
>>>> We've gone through fixing several error messages during the compilation
>>>> within the src/ dir from the latest wgs-8.3rc2.tar.bz2 package.
>>>> At the end of the day we stopped on "undefined reference" errors on
>>>> static libraries (mainly libseq.a, please see make_progs.log file).
>>>>
>>>> The 'gmake install' command within the kmer/ dir ran just fine.
>>>>
>>>> The following indicates BGQ OS type:
>>>> [erv3@bgq-fn src]$ uname -a
>>>> Linux bgq-fn.rcsg.rice.edu 2.6.32-431.el6.ppc64 #1 SMP Sun Nov 10
>>>> 22:17:43 EST 2013 ppc64 ppc64 ppc64 GNU/Linux
>>>>
>>>> We also had to edit c_make.as file, adding some -I options (to
>>>> indicate paths to libraries) on the CFLAGS fields from the "OSTYPE, Linux"
>>>> section.
>>>>
>>>> Running "make objs" and "make libs" separately, everything appeared to
>>>> work fine (see attached files make_objs.log and make_libs.log).
>>>> The above mentioned trouble came up on the "make progs" final command
>>>> we ran (make_progs.log file).
>>>>
>>>> Well, just to let you guys know and to see whether some light can be
>>>> shed.
>>>>
>>>> Thanks a lot,
>>>> Cheers,
>>>> Elton
>>>>
>>>> PS: I also noticed about the MPI cluster system on BGQ, Brian. So, do
>>>> you think it isn't worthwhile keeping the attempt to install CA on BGQ?
>>>>
>>>>
>>>>
>>
>>
>> --
>> Elton Vasconcelos, DVM, PhD
>> Post-doc at Verjovski-Almeida Lab
>> Department of Biochemistry - Institute of Chemistry
>> University of Sao Paulo, Brazil
>>
>>
>
>


-- 
Elton Vasconcelos, DVM, PhD
Post-doc at Verjovski-Almeida Lab
Department of Biochemistry - Institute of Chemistry
University of Sao Paulo, Brazil