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  • ians
    Member
    • Aug 2011
    • 53

    #1

    SOAP denovo seg faults during map

    Hi all,
    I'm getting a seg fault while running map during a SOAP denovo run. I'm running on OSX with SOAPdenovo v 1.05.
    I have checked to be sure input data has reads larger than 30 bp and that no empty lines exist. Does anyone have any other debugging ideas?

    Here is my cfg:

    max_rd_len=70
    [LIB]
    rank=1
    avg_ins=200
    reverse_seq=0
    asm_flags=3
    q1=s_1_1.fastq
    q2=s_1_2.fastq


    Here's the map execution:

    map -s soap.cfg -g test
    K = 23
    contig len cutoff: 25

    there're 3424 contigs in file: test, max seq len 60625, min seq len 24, max name len 10
    time spent on parse contigs file 0s
    8 thread created
    time spent on hash reads: 1s
    4517379 nodes allocated, 5614229 kmer in reads, 5614229 kmer processed
    time spent on De bruijn graph construction: 1s

    time spent on mapping long reads: 0s

    In file: soap.cfg, max seq len 70, max name len 256

    8 thread created
    5450 edges in graph
    basicContigInfo: 2 vs 3
    basicContigInfo: 3 vs 5
    basicContigInfo: 5 vs 7
    basicContigInfo: 7 vs 9
    ......
    basicContigInfo: 4331 vs 5457
    basicContigInfo: 4333 vs 5459
    basicContigInfo: 4334 vs 5461
    Segmentation fault
  • ians
    Member
    • Aug 2011
    • 53

    #2
    I've been troubleshooting now by trying to divide and conquer. I've been halving the data set to see if i can get one to not seg fault. However, this strategy has really got me scratching my head. I can get the top 1st 1/4 and 2nd 1/4 to get past map. However, the top 1/2 fails. Also, when I concatenate the 1st and 2nd 1/4, it also fails (cmp shows this concat with the top 1/2 are identical).

    Does anyone have ideas??

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