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  • SOAPdenovo-Trans: Seg fault

    Hi guys,
    today i tried SOAPdenovo-trans to assemble some Illumina paired-end reads. I have 3 sets from 3 different conditions. 2 of the sets finished without a glitch. But the 3rd set just does not want to proceed. the program exits with a seg fault and no any other error msg. I found it crashes at the first stage:

    -------------------------
    SOAPdenovo-Trans-31mer pregraph -K 31 -s config -o soap_out

    The version 1.0: released on Nov 12th, 2011

    In config, 1 libs, max seq len 76, max name len 256

    8 thread created
    read from file:
    read1.fastq
    read from file:
    read2.fastq
    Segmentation fault
    ------------------------

    Was digging on the net but found only hints about the length of the reads. Namely i had to check if all the reads are longer than 31bp. So i wrote a script and it seems all of them are longer than that. They are all 76bp.
    Also its not a memory issue as i have 64Gb on my machine and i see the program crashes before it even reaches 20Gb of used RAM.
    I also tried to reduce the k-mer to 29 but it crashes again, the same if i use SOAPdenovo-Trans-127mer with -K 31.

    I have no idea how to proceed further tho.

    I would appreciate any idea or hint on how to debug that!

    Thank you!

    PS: forgot to mention. My config is like that:
    ------------------------
    max_rd_len=76
    [LIB]
    avg_ins=280
    rank=1
    q1=read1.fastq
    q2=read2.fastq
    asm_flag=3
    reverse_seq=0

  • #2
    Hi there!

    I oberserve similar problems. I have preprocessed Illimina PE RNA-seq data where I merged overlapping paired-end reads. I filtered out short reads and removed all reads containing Ns since SOAPdenovo-trans doesnt seem to like that. I still run into segfaults. Any ideas on how to put SOAPdenovo-trans into positive mood?

    Comment


    • #3
      Hi everyone, i'm trying to run a SOAPdenovo-trans assembly but i don't know how to use de configuration file and finally execute the assembly, i don't know about the details of the file like the meaning of max_rd_len, avg_ins, rank, asm_flag, reverse_seq. Could you help me with this?

      Best regards!

      Comment


      • #4
        Hi kenietz and mariof. I have exactly the same problem. I was running soapdenovotrans for 25 Illumina libraries together in a machine with 200Gb RAM and it crashed reaching 4Gb of RAM... so I donĀ“t know what it is going on... mariof, do we know each other maybe?

        Comment


        • #5
          Was SOAPdenovo compiled with 64-bit support on the machine you are trying to run it on?

          Comment


          • #6
            Originally posted by kenietz View Post
            Hi guys,
            today i tried SOAPdenovo-trans to assemble some Illumina paired-end reads. I have 3 sets from 3 different conditions. 2 of the sets finished without a glitch. But the 3rd set just does not want to proceed. the program exits with a seg fault and no any other error msg. I found it crashes at the first stage:

            -------------------------
            SOAPdenovo-Trans-31mer pregraph -K 31 -s config -o soap_out

            The version 1.0: released on Nov 12th, 2011

            In config, 1 libs, max seq len 76, max name len 256

            8 thread created
            read from file:
            read1.fastq
            read from file:
            read2.fastq
            Segmentation fault
            ------------------------
            Hi all,
            According to my recent experience at Soapdenovo2 assembler, I found the Core dumpe (Seg fault) would have some relations with the input data.
            When I conducted Soapdenovo assembly using PE reads with quality filtering(fastx,q30p90), 5'-end (first 12nt) and adapters trimmg, everything was ok (N50 was 2K).
            Then, I did errors correction and trimming (seems trim the 3'-end) by using Soapec (parameters:-k 17 –x 8 –r 60 -Q 33), and Seg fault problem arised from 1st stage of Soapdenovo2.
            Is there anyone can explain why this happened?
            I'm a PhD candidate in rice breeding and absolutely a newcomer to NGS, I'm trying to detect SVs/CNVs between several rice cultivars through de novo assembly (all samples' raw reads would be ~35 fold in depth). If someone can give me some suggestions ?
            Thank you for anyone's patiently answering.
            Last edited by lovenlong; 05-31-2013, 06:25 PM.

            Comment

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