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  • 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

  • #2
    Hi Milo,

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

    Comment

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