Wednesday, October 5, 2011

SOAPdenovo: free(): invalid pointer:

I struggled with SOAPdenovo for 3 hours today. It was crashing at pregraph, shortly after parsing files for the first time. I singled it down to 1 file:

SOAPdenovo31mer pregraph -s test_05.cfg -o test_05 -p 24

Version 1.3: released on Nov 23th, 2009

In test_05.cfg, 1 libs, max seq len 1195, max name len 256

24 thread created
read from file:
 test_1.fa
time spent on hash reads: 10s, 129244 reads processed
[LIB] 0, avg_ins 10000, reverse 1 
22311858 nodes allocated, 12022388 kmer in reads, 12022388 kmer processed
*** glibc detected *** SOAPdenovo31mer: free(): invalid pointer: 0x00000000089b0203 ***
======= Backtrace: =========
[0x44cd16]
[0x450857]
[0x40472d]
[0x400316]
[0x434e93]
[0x440250]
[0x4001b9]
======= Memory map: ========
00400000-004d4000 r-xp 00000000 08:01 25826017                           /usr/local/bin/SOAPdenovo
006d4000-006d6000 rw-p 000d4000 08:01 25826017                           /usr/local/bin/SOAPdenovo
006d6000-00750000 rw-p 00000000 00:00 0 
026d3000-08a5e000 rw-p 00000000 00:00 0                                  [heap]
41810000-41811000 ---p 00000000 00:00 0 
.....

Turns out the problem wasn't my input, but my configuration settings. The library had reverse_seq=1 for a single-read fasta file. Returning reverse_seq=0 fixed my problem...

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