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  • SOAPdenovo2 long run

    Hello all,
    I’m trying to assemble a plant genome (this is my first time). I have 100bp PE reads (106G forward and 106G reverse). I’m using soapdenovo2 to assemble the data on a cluster. The job was running on 10 nodes with each using 20 threads and 80Gb of memory. The maximum amount of time allowed for a job is 7 days.
    I tried the following script however the job does not finish in the allotted time
    SOAPdenovo-63mer all -s ./soap.config -K 63 -R -o genome

    So then I tried to build it in parts using the script below, but even this does not finish
    SOAPdenovo-63mer pregraph -s ./soap.config -K 63 -R -o genome

    If using more computer resources or getting my time limit extended is not an option, how can I assemble the genome?

    I tried using DMTCP to checkpoint the run so that I can resubmit the run and continue the assembly after the 7 days but I cannot get DMTCP to work with soapdenovo2.

    I would be grateful for any assistance
    Cheers

  • #2
    I'd try a speedy assembler like BBtools tadpole.sh as a first pass just to see what a rough draft looks like. A slower assembler but one that should finish in a day is abyss-pe with the bloom filter option enabled.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      Thanks for the suggestions. I'll give these tools a try

      Comment

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