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  • Segmentation fault Error Soap2 mapping pairedend reads

    Hello everybody,

    we are a small team of Bioinformatitions working on some Illumina Paired end reads (HiSeq) (Fastq format)

    We are using Soap2 for the mapping approach and are giving Soap2 the following parameters:

    ../mapper/soap2.21release/soap -D index_aperea_G2A/reference_cavia_aperea_G2A.fa.index -a ../convertedreadsCtoT_Tier1read1.fq -b ../convertedreadsGtoA_Tier1read2.fq -o index_aperea_G2A/out-C2T_diff_l10_m100_x600.sop -2 index_aperea_G2A/unpaired-C2T_diff_l10_m100_x600.sop -u index_aperea_G2A/unmapped-C2T_diff_l10_m100_x600.sop -p 30 -m 100 -x 600 -l 10

    We have problems while using the -l 10 parameter at the end, we always get a segmentation fault. We already tried the mapping with 50 GB of memory, the segmentation fault remains. We are mapping against a mammalian genome. Strangely -l 15 is working. (The -l parameter defines the seedlength of each read). The error appears just a few seconds after the start. The output file gives "Begin allignment..." as the last working step.
    Thank you so much for your help!

    Cheers Tino

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