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Old 08-18-2014, 10:58 AM   #1
milo0615
Member
 
Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default SOAPDenovo-Trans Error - Abored (Core Dumped)

Hello,

I am trying to de novo assemble a small SOLiD file with SOAPDenovo-Trans but I get the following error:

./SOAPdenovo-Trans-31kmer all -K 31 -p 8 -s config -o Diplomat

The version 1.02: released on Sep 19th, 2012

pregraph -s config -K 31 -p 8 -o Diplomat
In config, 1 libs, max seq len 150, max name len 256

8 thread created
read from file:
/home/youngsook/Desktop/AdapterTrimmingTest2/Diplomat_F3.fastq
time spent on hash reads: 39s, 32102197 reads processed
[LIB] 0, avg_ins 259, reverse 0
0 nodes allocated, 0 kmer in reads, 0 kmer processed
*** glibc detected *** ./SOAPdenovo-Trans-31kmer: free(): invalid next size (normal): 0x0000000002486cf0 ***
======= Backtrace: =========
[0x47c7eb]
[0x480896]
[0x420740]
[0x41db21]
[0x414d98]
[0x459100]
[0x4001b9]
======= Memory map: ========
00400000-00507000 r-xp 00000000 fc:00 8520355 /home/youngsook/Downloads/SOAPdenovo-Trans1.02/SOAPdenovo-Trans-31kmer
00706000-00708000 rw-p 00106000 fc:00 8520355 /home/youngsook/Downloads/SOAPdenovo-Trans1.02/SOAPdenovo-Trans-31kmer
00708000-0075c000 rw-p 00000000 00:00 0
02485000-0a404000 rw-p 00000000 00:00 0 [heap]
40249000-4024a000 ---p 00000000 00:00 0
4024a000-40a4a000 rw-p 00000000 00:00 0 [stack:19277]
40a4a000-40a4b000 ---p 00000000 00:00 0
40a4b000-4124b000 rw-p 00000000 00:00 0 [stack:19279]
413cd000-413ce000 ---p 00000000 00:00 0
413ce000-41bce000 rw-p 00000000 00:00 0 [stack:19276]
41bce000-41bcf000 ---p 00000000 00:00 0
41bcf000-41bd2000 rw-p 00000000 00:00 0 [stack:19283]
41e53000-41e54000 ---p 00000000 00:00 0
41e54000-42654000 rw-p 00000000 00:00 0 [stack:19275]
42654000-42655000 ---p 00000000 00:00 0
42655000-42e55000 rw-p 00000000 00:00 0 [stack:19278]
42e55000-42e56000 ---p 00000000 00:00 0
42e56000-43656000 rw-p 00000000 00:00 0 [stack:19280]
43656000-43657000 ---p 00000000 00:00 0
43657000-43e57000 rw-p 00000000 00:00 0 [stack:19281]
43e57000-43e58000 ---p 00000000 00:00 0
43e58000-44658000 rw-p 00000000 00:00 0 [stack:19282]
7fa37218a000-7fa37218b000 rw-p 00000000 00:00 0
7fff17589000-7fff175aa000 rw-p 00000000 00:00 0 [stack]
7fff175fe000-7fff17600000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)


Can anyone assist me with this error? What is the workaround it?

Thank you for your help.


-Milo
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Old 09-03-2014, 12:33 AM   #2
longbow0
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Location: CN

Join Date: Dec 2012
Posts: 2
Default

Hi Milo,

Have you tried to download the SOAPdenovo-Trans source code and compile locally?
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