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  • Error during bowtie2-align run , (ERR): bowtie2-align exited with value 139

    I have a pipleline written in python that calls bowtie2-align. I am using bowtie2-align to align the same fastq.gz file against a set of amplicons.

    I am testing the run on three machines with the exact same data

    1) Linux box, Ubuntu 14.04 ,48 GB memory , everything works
    2) Linux box2 ozy,Ubuntu 14.04 , 32 GB memory , segfaults with err 139
    3) Macbook Pro, OSX 10.10.3 , 16 GB memory , everything works

    The details of the bowtie2 on the working and non-working Linux box ( both had the same one) are given below.
    On Linux box2 ozy, bowtie2-align crashes with the message:

    Code:
    Segmentation fault (core dumped)
    (ERR): bowtie2-align exited with value 139
    On this machine , I also tested with a compiled from source bowtie2 ( v 2.2.5 ) and it gave the same error (Value 139).

    The command I am using for bowtie2 in all cases is :

    Code:
    align_cmd = 'bowtie2 --very-sensitive -k 2 -x amplicons -1 %s -2 %s -S initial_aligns.sam' % (read1_fastq, read2_fastq)
    Can someone give me pointers on how to troubleshoot why the crash happens on only one machine and not the other two ?.

    Thanks
    Hari

    hari@ozy:~$ bowtie2 --version
    /usr/bin/bowtie2-align version 2.1.0
    64-bit
    Built on roseapple
    Tue Jun 25 17:45:14 UTC 2013
    Compiler: gcc version 4.8.1 (Ubuntu 4.8.1-4ubuntu2)
    Options: -O3 -m64 -msse2 -funroll-loops -g3 -Wl,-Bsymbolic-functions
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}



    The compiled from source bowtie2 gives same error on Linux box 2:

    hari@ozy:~/DEmultiplexed/analysis/VEGF1_S1$ bowtie2 --version
    /home/hari/bowtie2-2.2.5/bowtie2-align-s version 2.2.5
    64-bit
    Built on ozymandias
    Sun Apr 19 10:48:02 EDT 2015
    Compiler: gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
    Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

    There Linux machines also have different kernel versions.

    Working Kernel:
    hari@UBUNTU01:~$ uname -a
    Linux UBUNTU01 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux


    Segfault kernel:
    hari@ozy:~$ uname -a
    Linux ozymandias 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
    Last edited by harijay; 04-19-2015, 09:45 AM.

  • #2
    The only general way to debug this is to run bowtie2-align-s in a debugger (I think there's a bowtie2-align-debug-s or something like that that can be used for this purpose). I wonder if there's some quirky library on the "ozy" machine that's causing the segfault.

    Comment


    • #3
      Same issue...

      Hi harijay

      Were you able to resolve this issue?

      I'm having much the same problem. I have recently reinstalled my computer with Ubuntu 16.10 (Kubuntu) and installed Bowtie2 by running:
      sudo apt-get install bowtie2

      This works well and installs v. 2.2.9-4.

      When I try to do an alignment, however I get an error-message after a short while:
      Segmentation fault (core dumped)
      (ERR): bowtie2-align exited with value 139

      This also occurs when I try to rerun a previously made alignment using the same files and same command that worked on a previous installation, so it seems that something is wrong with the current installation. I have also downloaded the pre-compiled v. 2.3.0 but get the same message.

      There is actually generated a truncated sam file ending abruptly like this:
      ...
      @SQ SN:ENST00000557887.1 LN:2606
      @SQ SN:ENST00000564967.1 LN:2199
      @SQ SN:ENST00



      Originally posted by harijay View Post
      I have a pipleline written in python that calls bowtie2-align. I am using bowtie2-align to align the same fastq.gz file against a set of amplicons.

      I am testing the run on three machines with the exact same data

      1) Linux box, Ubuntu 14.04 ,48 GB memory , everything works
      2) Linux box2 ozy,Ubuntu 14.04 , 32 GB memory , segfaults with err 139
      3) Macbook Pro, OSX 10.10.3 , 16 GB memory , everything works

      The details of the bowtie2 on the working and non-working Linux box ( both had the same one) are given below.
      On Linux box2 ozy, bowtie2-align crashes with the message:

      Code:
      Segmentation fault (core dumped)
      (ERR): bowtie2-align exited with value 139
      On this machine , I also tested with a compiled from source bowtie2 ( v 2.2.5 ) and it gave the same error (Value 139).

      The command I am using for bowtie2 in all cases is :

      Code:
      align_cmd = 'bowtie2 --very-sensitive -k 2 -x amplicons -1 %s -2 %s -S initial_aligns.sam' % (read1_fastq, read2_fastq)
      Can someone give me pointers on how to troubleshoot why the crash happens on only one machine and not the other two ?.

      Thanks
      Hari

      hari@ozy:~$ bowtie2 --version
      /usr/bin/bowtie2-align version 2.1.0
      64-bit
      Built on roseapple
      Tue Jun 25 17:45:14 UTC 2013
      Compiler: gcc version 4.8.1 (Ubuntu 4.8.1-4ubuntu2)
      Options: -O3 -m64 -msse2 -funroll-loops -g3 -Wl,-Bsymbolic-functions
      Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}



      The compiled from source bowtie2 gives same error on Linux box 2:

      hari@ozy:~/DEmultiplexed/analysis/VEGF1_S1$ bowtie2 --version
      /home/hari/bowtie2-2.2.5/bowtie2-align-s version 2.2.5
      64-bit
      Built on ozymandias
      Sun Apr 19 10:48:02 EDT 2015
      Compiler: gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
      Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY
      Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

      There Linux machines also have different kernel versions.

      Working Kernel:
      hari@UBUNTU01:~$ uname -a
      Linux UBUNTU01 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux


      Segfault kernel:
      hari@ozy:~$ uname -a
      Linux ozymandias 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

      Comment

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