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  • Segmentation fault (core dumped) in Velvet

    Hi all,

    I am using MiSeq paired end data which I recived from our sequencing facility, this data had already been cleaned using sythe and sickle. I have put the data through Fastqc to check the quality and revieved the following information:

    File type Conventional base calls
    Encoding Sanger / Illumina 1.9
    Total Sequences 1270012
    Filtered Sequences 0
    Sequence length 20-251

    I want to use Velvet as it seems to be the program used in most papers from within my field. I have installed Velvet from the ubuntu software center as I am not very skilled in using termial commands. It appeares to be the same version as from the velvet website (1.2.10).

    The problem I have is that when I attempt to use velveth I get a segmentation fault.

    Code:
    shell@shell-MS-1727:~$ velveth VPI_21 21 -shortPaired -fastq -separate VPI_R1.fastq VPI_R2.fastq
    Segmentation fault (core dumped)
    I have reinstalled ubuntu as I read that I might have caused an issue when using a chmod command when following a "teach youself linux" book but this has not helped fix the issue.

    I have also tried:

    Code:
    sudo apt-get install velvet
    Reading package lists... Done
    Building dependency tree       
    Reading state information... Done
    velvet is already the newest version.
    0 to upgrade, 0 to newly install, 0 to remove and 10 not to upgrade.
    I have very little linux experiance and so I am not sure:
    A) What this error means
    B) How to fix it.

    Any help would be greatly appreciated.

  • #2
    Are you using a virtual machine for running ubuntu? How much memory have you assigned to the VM if this is a virtual machine? Are you running 32-bit or 64-bit version of ubuntu.

    Wikipedia has a simple intro for Seg Faults in first paragraph: http://en.wikipedia.org/wiki/Seg_fault

    Comment


    • #3
      I am not using a vertual machine. I am running 64-bit version 14.04 LTS, with 3.8GiB memory.
      Thank you for the link I will have a read over it.

      Comment


      • #4
        Does the seg fault occur right away or the program runs for some time before crashing?

        If you just run

        Code:
        $velveth -h
        do you get the help output?

        Comment


        • #5
          The crash occurs right away I get no other outputs only the error message.

          If I run "$velveth -h" I do get the help output.

          Comment


          • #6
            Do you have any other data you can use to test the velvet install?

            Comment


            • #7
              Do you have any other data you can use to test the velvet install?
              Unfortunately not, is there anywhere I could get some? I had a quick look on the NCBI ftp website but couldn't see anything that didn't look like it had been assembled already.

              Comment


              • #8
                Originally posted by jellybaby83 View Post
                Unfortunately not, is there anywhere I could get some? I had a quick look on the NCBI ftp website but couldn't see anything that didn't look like it had been assembled already.
                There is a test set you can use on this page: http://ged.msu.edu/angus/beacon-2012...vet-ecoli.html

                Comment


                • #9
                  Thank you GenoMax I will try with that.

                  I found a single read file on

                  ftp://ftp-trace.ncbi.nih.gov/1000gen...sequence_read/

                  I used:

                  Code:
                  velveth test_21 21 -short -fastq SRR642626.filt.fastq
                  Segmentation fault (core dumped)
                  But still have the same error message

                  Comment


                  • #10
                    I am going to suggest that you download velvet source code and compile the program yourself.

                    Comment


                    • #11
                      Ok thanks for all your help

                      Comment

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