Re: [Inchworm-users] inchworm runtimes

[Brian J H. <bh...@br...>]

Hi Dana,

Sounds like so far, so good.

In the trinity/ folder, you can see if inchworm has started reporting any
contigs yet.  There's also a monitor.out file there that will track the
current status, in case it's not reporting contigs yet.

In the future, you can set the OMP_NUM_THREADS environmental variable to 4
to use only 4 threads in the initial phase, rather than consuming whatever
it can grab on to.   In the next version of Trinity, I'll make this a
command-line option.

Let me know how it goes.

Best,

-brian


On Tue, Mar 22, 2011 at 4:16 PM, Dana Price <dan...@gm...> wrote:

>
> I've got 42 million Illumina paired end reads (84 million total) of
> 125x125bp, and ran the trinity pipeline via
>
> /usr/local/bin/Trinity.pl --seqType fq --left left.fastq --right
> right.fastq  --output output --run_butterfly --num_butterfly_CPU 48
> --min_contig_length 100
>
> It's running inchworm, via
>
> /usr/local/bin/Inchworm/bin/inchworm --reads both.fa --run_inchworm -K 25
> -L 48 --monitor 1  --DS  2>monitor.out > inchworm.K25.L48.DS.fa
>
> That's been running for 3 days on a 48 cpu AMD Opteron 2.1GHz SMP machine.
> It spawned 48 threads for the first two days.  Today I see that the number
> of threads has dropped to 1.  It's got a 74 gig memory footprint.  I'm
> wondering if it's still doing anything?  Is a three day assembly
> par-for-the-course with this much data?
>
> Thanks!
>
>
> --
> Dana Price
> Laboratory Researcher in Bioinformatics
> Rutgers, The State University
> Bhattacharya Lab
> http://dblab.rutgers.edu
>
>
>
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-- 
-- 
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas