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  • running soap denovo

    Hi,
    I am trying to run SOAP Denovo, and I am following their manual instructions to run the example. Here is the command I am using:

    ./SOAPdenovo-63mer pregraph -s ecoli2.config -K 36 -p 8 -o testOut.txt

    the contents of ecoli2.config are:
    "q=/home/pyang/soapDenovo/SOAPdenovo-V1.05/bin/s_1_1_sequence.fastq"

    However, I keep getting a segmentation fault for the output:

    Version 1.05: released on July 29th, 2010

    K should be an odd number
    In ecoli2.config, 0 libs, max seq len 100, max name len 256

    8 thread created
    time spent on hash reads: 0s, 0 reads processed
    0 nodes allocated, 0 kmer in reads, 0 kmer processed
    0 linear nodes
    time spent on marking linear nodes 0s
    time spent on pre-graph construction: 0s

    deLowKmer 0, deLowEdge 0
    Start to remove tips of single frequency kmers short than 74
    0 tips off
    8 thread created
    0 linear nodes
    Start to remove tips which don't contribute the most links
    kmer set 0 done
    kmer set 1 done
    kmer set 2 done
    kmer set 3 done
    kmer set 4 done
    kmer set 5 done
    kmer set 6 done
    kmer set 7 done
    0 tips off
    8 thread created
    0 linear nodes
    time spent on cutTipe: 0s

    0 (0) edges 0 extra nodes
    time spent on making edges: 0s

    In file: ecoli2.config, max seq len 100, max name len 256

    8 thread created
    Segmentation fault


    Can someone help me with this?? Thanks!!!

  • #2
    As the program says, you have to make k an odd number, so try 35 or 37 instead of 36. Something about the algorithm not liking palindromes.

    Not sure if that caused the segmentation fault, but it couldn't hurt.

    Comment


    • #3
      Segmentation problem

      Hi Sweet DNA girl
      Didi you find a solution to your problem? I'm having the same problem
      Cheers,
      Niloofar

      Comment


      • #4
        hye,

        Someone find a solution ?

        Thanks.

        Comment


        • #5
          running soap denovo

          segmentation faults often happen when the computer runs out of memory,
          and de novo assembly can use quite a lot of memory.

          Comment


          • #6
            But when i try in the cluster, i have this output without segmentation fault:

            ********************
            Pregraph
            ********************

            Parameters: pregraph -s test_solexa.config -R -o assembly_SOAP

            In test_solexa.config, 2 lib(s), maximum read length 76, maximum name length 256.

            8 thread(s) initialized.
            Time spent on hashing reads: 0s, 0 read(s) processed.
            LIB(s) information:
            [LIB] 0, avg_ins 76, reverse 1.
            [LIB] 1, avg_ins 76, reverse 1.
            0 node(s) allocated, 0 kmer(s) in reads, 0 kmer(s) processed.
            done hashing nodes
            0 linear node(s) marked.
            Time spent on marking linear nodes: 0s.
            Time spent on pre-graph construction: 1s.

            Start to remove frequency-one-kmer tips shorter than 46.
            Total 0 tip(s) removed.
            8 thread(s) initialized.
            0 linear node(s) marked.
            Start to remove tips with minority links.
            0 tip(s) removed in cycle 1.
            Total 0 tip(s) removed.
            8 thread(s) initialized.
            0 linear node(s) marked.
            Time spent on removing tips: 0s.

            0 (0) edge(s) and 0 extra node(s) constructed.
            Time spent on constructing edges: 0s.

            In file: test_solexa.config, max seq len 76, max name len 256.
            8 thread(s) initialized.
            0 read(s) processed.
            Time spent on:
            importing reads: 0s,
            chopping reads to kmers: 0s,
            searching kmers: 0s,
            aligning reads to edges: 0s,
            searching (K+1)mers: 0s,
            adding pre-arcs: 0s,
            recording read paths: 0s.
            0 marker(s) output.
            Reads alignment done, 0 read(s) deleted, 0 pre-arc(s) added.
            LIB(s) information:
            [LIB] 0, avg_ins 76, reverse 1.
            [LIB] 1, avg_ins 76, reverse 1.
            Time spent on aligning reads: 0s.

            0 vertex(es) output.
            Overall time spent on constructing pre-graph: 0m.

            Comment


            • #7
              I had a similar problem. My solution was to go back to the SOAPdenovo2 Sourceforge page and download the separate bin folder that is available. The executables in the downloaded bin worked for me instead of the ones in the src download.

              Comment

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