tack smashing detected ***: bwa terminated

[Imbeaud]

Hi,

I have a problem with the BWA...
Here is the command line and error message is below
bwa sampe virusbwaidx R1.sai R2.sai '/MD1200/BWA/Sample/Sample_CHC1154T_R1_fastq.txt.gz' '/MD1200/BWA/Sample/Sample_CHC1154T_R2_fastq.txt.gz' > output.sam

I am not sure to understand what is going on?
Can anyone help me to solve this issue?

Kind Reards

/ Sandrine


*** stack smashing detected ***: bwa terminated
======= Backtrace: =========
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x3950b01d47]
/lib64/libc.so.6(__fortify_fail+0x0)[0x3950b01d10]
bwa[0x4086d3]
bwa[0x408795]
bwa[0x416c1d]
bwa[0x417595]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3950a1ecdd]
bwa[0x401949]
======= Memory map: ========
00400000-0042e000 r-xp 00000000 fd:00 281878 /usr/bin/bwa
0062e000-00631000 rw-p 0002e000 fd:00 281878 /usr/bin/bwa
01c5d000-020e0000 rw-p 00000000 00:00 0 [heap]
36d3800000-36d3815000 r-xp 00000000 fd:00 1835467 /lib64/libz.so.1.2.3
36d3815000-36d3a14000 ---p 00015000 fd:00 1835467 /lib64/libz.so.1.2.3
36d3a14000-36d3a15000 r--p 00014000 fd:00 1835467 /lib64/libz.so.1.2.3
36d3a15000-36d3a16000 rw-p 00015000 fd:00 1835467 /lib64/libz.so.1.2.3
3950600000-3950620000 r-xp 00000000 fd:00 1835062 /lib64/ld-2.12.so
395081f000-3950820000 r--p 0001f000 fd:00 1835062 /lib64/ld-2.12.so
3950820000-3950821000 rw-p 00020000 fd:00 1835062 /lib64/ld-2.12.so
3950821000-3950822000 rw-p 00000000 00:00 0
3950a00000-3950b89000 r-xp 00000000 fd:00 1835064 /lib64/libc-2.12.so
3950b89000-3950d89000 ---p 00189000 fd:00 1835064 /lib64/libc-2.12.so
3950d89000-3950d8d000 r--p 00189000 fd:00 1835064 /lib64/libc-2.12.so
3950d8d000-3950d8e000 rw-p 0018d000 fd:00 1835064 /lib64/libc-2.12.so
3950d8e000-3950d93000 rw-p 00000000 00:00 0
3951200000-3951217000 r-xp 00000000 fd:00 1835072 /lib64/libpthread-2.12.so
3951217000-3951417000 ---p 00017000 fd:00 1835072 /lib64/libpthread-2.12.so
3951417000-3951418000 r--p 00017000 fd:00 1835072 /lib64/libpthread-2.12.so
3951418000-3951419000 rw-p 00018000 fd:00 1835072 /lib64/libpthread-2.12.so
3951419000-395141d000 rw-p 00000000 00:00 0
3951600000-3951683000 r-xp 00000000 fd:00 1835085 /lib64/libm-2.12.so
3951683000-3951882000 ---p 00083000 fd:00 1835085 /lib64/libm-2.12.so
3951882000-3951883000 r--p 00082000 fd:00 1835085 /lib64/libm-2.12.so
3951883000-3951884000 rw-p 00083000 fd:00 1835085 /lib64/libm-2.12.so
395d200000-395d216000 r-xp 00000000 fd:00 1835445 /lib64/libgcc_s-4.4.6-20120305.so.1
395d216000-395d415000 ---p 00016000 fd:00 1835445 /lib64/libgcc_s-4.4.6-20120305.so.1
395d415000-395d416000 rw-p 00015000 fd:00 1835445 /lib64/libgcc_s-4.4.6-20120305.so.1
7faa920b5000-7faa9223e000 rw-p 00000000 00:00 0
7faa92254000-7faa92256000 rw-p 00000000 00:00 0
7fff52af4000-7fff52b09000 rw-p 00000000 00:00 0 [stack]
7fff52bff000-7fff52c00000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Abandon

[GenoMax]

What OS is this on (32-bit/64-bit)? Did you compile bwa on this machine?

[Imbeaud]

Hi,

Oups sorry
Linux x64
BWA was compile on this machine et worked perfectly during my yesterday tried on chr1.fa...

I'm not sure to understand the error message... Is that due to memory issues or too long character string in command lines, or other?

Kind Regards
/ Sandrine

[GenoMax]

Stack smashing refers to buffer overflows (http://en.wikipedia.org/wiki/Stack_smashing). How much memory do you have on this machine?

[Imbeaud]

Scientific Linux
2.6.23-358.6.1.el6.x86_64
GNOME 2.28.2
126 Go RAM
40 CPU (2.13 GHz)

[GenoMax]

Heng Li (lh3) is on this forum regularly. Hopefully he will have something to say.

Can you post the output of?

$ ldd /path_to/bwa

Can you also check that your job with "chr1" still works?

[Imbeaud]

[]# ldd '/usr/bin/bwa'
linux-vdso.so.1 => (0x00007fffb98b6000)
libm.so.6 => /lib64/libm.so.6 (0x0000003951600000)
libz.so.1 => /lib64/libz.so.1 (0x00000036d3800000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003951200000)
libc.so.6 => /lib64/libc.so.6 (0x0000003950a00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003950600000)


I am re-running the Chr1.. Waiting for the end... I will let you know.. In the meantime, any advice is welcome.

Kind regards
/ Sandrine