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  • soap2 segmentation fault when loading index table

    Hi all,

    I try to use soap2 to align PE reads from HiSeq2000. Each read file is about 25GB. I have had very little luck with soap aligner.

    I used 2twt-builder to build the index files first on hg19.fa, which took quote a while, then called:

    soap -a s_5_1_testN.fq -b s_5_2_testN.fq -D /genomes/human/hg19/soap/hg19.fa.index -o mapped.soap -2 se.soap -m 140 -x 400 -p 2


    Begin Program SOAPaligner/soap2
    Fri Feb 25 16:30:06 2011
    Reference: /genomes/human/hg19/soap/hg19.fa.index
    Query File a: s_5_1_testN.fq
    Query File b: s_5_2_testN.fq
    Output File: mapped.soap
    se.soap
    Load Index Table ...
    Segmentation fault

    The machine has sufficient available memory. Did I build the index files incorrectly? Anyone had the same kind of problem? Thanks a lot for any insight on this.

  • #2
    Just a few minutes ago, I was puzzled by the same question. One probable reason is that the '2twt-builder' and the 'soap' are not from the same verion of soap package. Maybe you need check their paths using 'which 2twt-builder' and 'which soap'.

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