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  • error using transcriptomic data (transabyss)

    Hi ,

    I was trying to assemble transcriptomic datasets (using abyss) for creating initial assemblies to be given as input for transabyss.

    I got a segmentation fault.. (File attached with this thread)

    My command shell script

    #!/bin/bash
    #PBS -l ncpus=16
    #PBS -l walltime=100:00:00,vmem=60GB
    #PBS -j oe
    #PBS -A a07
    #PBS -wd
    ulimit -s unlimited

    time /usr/local/abyss/1.2.4-openmpi/bin/abyss-pe mpirun=/usr/local/openmpi/1.4.3/bin/mpirun np=16 n=5 k=55 s=200 name=plant lib='lib1' \ lib1='/project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_1_sequence.txt /project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_2_sequence.txt' OVERLAP_OPTIONS=--no-scaffold SIMPLEGRAPH_OPTIONS=--no-scaffold

    I will appreciate if anyone can put some light on this..

    cheers,

    Nandan
    I have been using this abyss installation fine for last few months with other genomic datasets..
    Attached Files

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