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  • 2seq
    Junior Member
    • Oct 2012
    • 9

    KmerFreq - std::bad_alloc

    I am new to SOAPdenovo and am still learning, so please help out this newbie.
    I am running a PBS script to run KmerFreq before running SOAP. I have two fq files: s_4_1.txt and s_4_2.txt which I list in the list file. I made sure to add a carriage return after the last file in the list. Both files are around 65G. I am running KmerFreq on 1 node and 1 processor and have allocated 100gb of memory. I'm also running this over valgrind so I can determine the needs of the program for some other samples. So the script looks like:

    #PBS -N KmerFreq-PL71 -l nodes=1pn=1,mem=100gb -j oe -m be -M [email protected]
    #PBS -l walltime=12:00:00
    module load valgrind
    module load soapdenovo-1.05
    cp * PFSDIR
    cd $PFSDIR
    valgrind --tool=massif KmerFreq -i PL_list -o PL71_correct
    cp * $PBS_O_WORKDIR

    In checking the log file, I see:
    ==7580==
    quality cutoff: 5
    seed length: 17
    output kmer index?: no
    file format: fq
    terminate called after throwing an instance of 'std::bad_alloc'
    what (): St9bad_alloc
    ==7580==
    -bash: line 7: 7580 aborted

    Any assistance would be greatly appreciated!

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