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  • Speeding Up Soapdenovo2

    Hi,
    I am working on some de novo assemblies with Soapdenovo2 with the multi-mer option, and wanted to know if anyone has experience with getting these crunched quickly-ish.
    Specifically, can Soap split itself over multiple nodes on a cluster (via SLURM)? All examples sbatch scripts I see have it use only one node and 8 cpus. I have access to more if it can use it.

    Details on what I'm running currently:

    My data: 33M (x2) reads of paired end Illumina, 150b read length on fragments in the 300-400bp range. Interleaved in a *.fa. Animal genome, estimating ~100-300Mb.

    Relevant SBATCH info:
    Code:
    #SBATCH --nodes=1
    #SBATCH --ntasks-per-node=8
    #SBATCH --time=40:00:00
    #SBATCH --mem-per-cpu=4000
    SOAPdenovo-63mer all -s MYCONFIG -K 63 -m 57 -R -o TESTRUN 1>TEST_ass.log 2>TEST_ass.err
    MYCONFIG:
    Code:
    max_rd_len=150
    [LIB]
    # most options just commented out, assuming defaults are fine for my short paired data
    avg_ins=350
    asm_flags=3
    rank=1
    p=TESTDATA.fa
    For Soapdenovo2, what's the best combination of resources to crank up? Nodes? ntasks (and correspondingly the -p parameter for my run command)? mem-per-cpu?

    Thank you!

  • #2
    Just for anyone wandering in later with a similar question, after getting some more info, we are trying this:


    #SBATCH --nodes=4
    #SBATCH --ntasks-per-node=8
    #SBATCH –-mem=128000
    #SBATCH --time=168:00:00


    Should be plenty to let SOAP do it's thing as quickly as it can, hopefully.

    Comment

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