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  • joyce kang
    Junior Member
    • Nov 2011
    • 5

    #1

    SOAPdenovo running error

    when I used soapdenovo, i got the following results:

    *********
    In /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, 1 libs, max seq len 100, max name len 256

    8 thread created
    time spent on hash reads: 0s, 0 reads processed
    [LIB] 0, avg_ins 2000, reverse 1
    0 nodes allocated, 0 kmer in reads, 0 kmer processed
    0 linear nodes
    time spent on marking linear nodes 0s
    time spent on pre-graph construction: 0s

    deLowKmer 0, deLowEdge 1
    Start to remove tips of single frequency kmers short than 46
    0 tips off
    8 thread created
    0 linear nodes
    Start to remove tips which don't contribute the most links
    kmer set 0 done
    kmer set 1 done
    kmer set 2 done
    kmer set 3 done
    kmer set 4 done
    kmer set 5 done
    kmer set 6 done
    kmer set 7 done
    0 tips off
    8 thread created
    0 linear nodes
    time spent on cutTipe: 0s

    0 (0) edges 0 extra nodes
    time spent on making edges: 0s

    In file: /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, max seq len 100, max name len 256

    8 thread created
    0 reads processed
    time 0,0,0,0,0,0,0
    0 markers outputed
    done mapping reads, 0 reads deleted, 0 arcs created
    [LIB] 0, avg_ins 2000, reverse 1
    time spent on mapping reads: 0s

    0 vertex outputed
    overall time for lightgraph: 0m
    *****************************
    it seems wrong. so can you help figure out the reason? thanks a lot.

    BTW, my command line is:./SOAPdenovo-127mer pregraph -s ~/SOAPdenovo-V1.05/test.config -o out
    and the config file is:
    max_rd_len=100
    [LIB]
    rank=2
    avg_ins=2000
    reverse_seq=1
    asm_flags=2
    q1=/bio/taupo/kang138/Dugong-COV-NGS-1_MPS017399_PELib_T_L005_R1_001.fastq
    q2=/bio/taupo/kang138/Dugong-COV-NGS-2_MPS017400_PELib_G_L006_R1_001.fastq

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