Standalone meme crashing when using -cons option

[Marco Galardini]

Hi,

we are having a problem with the latest version of meme (version 4.9.0_4), installed on Ubuntu 12.04.

This problem wasn't present with earlier versions (like 4.8.1).

When searching for a motif using a consensus sequence we get an error.

cmd line: meme -dna upstream3.faa -mod oops -nmotifs 1 -minw 14 -maxw 14 -cons TTGANNNNNNTCAA

output:

The output directory 'meme_out' already exists.

Its contents will be overwritten.

Initializing the motif probability tables for 2 to 6 sites...

nsites = 6

Done initializing

seqs=     6, min= 100, max=  239, total=      940

motif=1

em: w=  14, psites=   6, iter=   0

*** glibc detected *** meme: free(): invalid pointer: 0x0000000001fa68b0 ***

======= Backtrace: =========

/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb387ea5b96]

meme[0x406117]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb387e4876d]

meme[0x4066ed]

======= Memory map: ========

00400000-005c7000 r-xp 00000000 08:06 29103930                           /home/mgalardini/bin/meme.bin

007c6000-007ce000 r--p 001c6000 08:06 29103930                           /home/mgalardini/bin/meme.bin

007ce000-007d1000 rw-p 001ce000 08:06 29103930                           /home/mgalardini/bin/meme.bin

007d1000-00c22000 rw-p 00000000 00:00 0 

01f93000-0218e000 rw-p 00000000 00:00 0                                  [heap]

7fb387c11000-7fb387c26000 r-xp 00000000 08:06 22545450                   /lib/x86_64-linux-gnu/libgcc_s.so.1

7fb387c26000-7fb387e25000 ---p 00015000 08:06 22545450                   /lib/x86_64-linux-gnu/libgcc_s.so.1

7fb387e25000-7fb387e26000 r--p 00014000 08:06 22545450                   /lib/x86_64-linux-gnu/libgcc_s.so.1

7fb387e26000-7fb387e27000 rw-p 00015000 08:06 22545450                   /lib/x86_64-linux-gnu/libgcc_s.so.1

7fb387e27000-7fb387fdc000 r-xp 00000000 08:06 22578063                   /lib/x86_64-linux-gnu/libc-2.15.so

7fb387fdc000-7fb3881db000 ---p 001b5000 08:06 22578063                   /lib/x86_64-linux-gnu/libc-2.15.so

7fb3881db000-7fb3881df000 r--p 001b4000 08:06 22578063                   /lib/x86_64-linux-gnu/libc-2.15.so

7fb3881df000-7fb3881e1000 rw-p 001b8000 08:06 22578063                   /lib/x86_64-linux-gnu/libc-2.15.so

7fb3881e1000-7fb3881e6000 rw-p 00000000 00:00 0 

7fb3881e6000-7fb3882e1000 r-xp 00000000 08:06 22578071                   /lib/x86_64-linux-gnu/libm-2.15.so

7fb3882e1000-7fb3884e0000 ---p 000fb000 08:06 22578071                   /lib/x86_64-linux-gnu/libm-2.15.so

7fb3884e0000-7fb3884e1000 r--p 000fa000 08:06 22578071                   /lib/x86_64-linux-gnu/libm-2.15.so

7fb3884e1000-7fb3884e2000 rw-p 000fb000 08:06 22578071                   /lib/x86_64-linux-gnu/libm-2.15.so

7fb3884e2000-7fb388504000 r-xp 00000000 08:06 22578077                   /lib/x86_64-linux-gnu/ld-2.15.so

7fb38860d000-7fb3886d5000 rw-p 00000000 00:00 0 

7fb388700000-7fb388704000 rw-p 00000000 00:00 0 

7fb388704000-7fb388705000 r--p 00022000 08:06 22578077                   /lib/x86_64-linux-gnu/ld-2.15.so

7fb388705000-7fb388707000 rw-p 00023000 08:06 22578077                   /lib/x86_64-linux-gnu/ld-2.15.so

7fff2494f000-7fff24971000 rw-p 00000000 00:00 0                          [stack]

7fff249ff000-7fff24a00000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Aborted (core dumped)

Thanks for any help or suggestion you might have.

Marco

[CharlesEGrant]

It turns out that this problem was do to a bug in MEME. I've emailed you a patch that fixes the problem.

We'll also see that this fix gets in the next version of the MEME Suite software.

Thanks for taking the time to report the problem! Please let us know if you run into further problems.

Charles