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:
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 :
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
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
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)
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
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