treangen/metAMOS — Issue #36: bowtie segmentation fault
Author: koadman
Created: 2012-02-17 20:31:45+00:00
State: open

bowtie is segfaulting during the scaffold step on a CentOS 5 system with the following kernel:
`uname -a
Linux jumbo-0-1.merlot.genomecenter.ucdavis.edu 2.6.18-194.11.4.el5 #1 SMP Tue Sep 21 05:04:09 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux`

Running the exact same bowtie command using bowtie-0.12.7 downloaded from sourceforge completes without error.

I'm not sure whether it's relevant, but there appears to be a difference in which libs were linked. bowtie in metamos has:
`-bash-3.2$ ldd /home/koadman/software/metAMOS/Utilities/cpp/Linux-x86_64/bowtie
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000031d8c00000)
libm.so.6 => /lib64/libm.so.6 (0x00000031d9000000)
libc.so.6 => /lib64/libc.so.6 (0x00000031d8400000)
/lib64/ld-linux-x86-64.so.2 (0x00000031d8000000)
`

bowtie from sf.net has:

`-bash-3.2$ ldd ~/software/bowtie-0.12.7/bowtie
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000031d8c00000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000031db000000)
libm.so.6 => /lib64/libm.so.6 (0x00000031d9000000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000031dac00000)
libc.so.6 => /lib64/libc.so.6 (0x00000031d8400000)
/lib64/ld-linux-x86-64.so.2 (0x00000031d8000000)
-bash-3.2$ file ~/software/bowtie-0.12.7/bowtie
/home/koadman/software/bowtie-0.12.7/bowtie: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped
`