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aligning solid data with bwa -- Seg Fault

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  • drio
    replied
    That's not it. there are other reads with -1 in the quals that bwa process without problems.

    Leave a comment:


  • Chipper
    replied
    You need to remove the sign from the quality files (add "s/-//g;" after reading from the quality file in solid2fastq.pl).

    Leave a comment:


  • drio
    started a topic aligning solid data with bwa -- Seg Fault

    aligning solid data with bwa -- Seg Fault

    I am trying to align some SOLiD data with bwa and there are two reads
    that cause bwa to crash:

    Code:
    @1_10_531
    T.11011..010..31...20..300..301.00.0.30...200..0...
    +
    "7=<<8"":8:""28"""&%""62$""))&"%6"2"10"""7,1""#"""
    @1_10_536
    T.01300.3100..00...12..0000.000.0030.010.0300..0...
    +
    "77+03"9/,4""&4"""&+""1:)9"&)/"67&5">5'",5*2""="""
    I am using bwa (0.5.4).

    The indexing of the reference (human) was created using:

    bwa index -a bwtsw -c -p "cs" ./indexes

    For the alignment I used:

    bwa aln -t 8 -c $ref $reads > aln.fr.solid.sai
    bwa samse $ref aln.fr.solid.sai $reads > aln.fr.solid.sam

    bwa crashes dumping: 22550 Segmentation fault

    The original qualities are:

    >1_10_531_F3
    -1 22 28 27 27 23 -1 -1 25 23 25 -1 -1 17 23 -1 -1 -1 5 4 -1 -1 21 17 3 -1 -1 8 8 5 -1 4 21 -1 17 -1 16 15 -1 -1 -1 22 11 16 -1 -1 2 -1 -1 -1
    >1_10_536_F3
    -1 22 22 10 15 18 -1 24 14 11 19 -1 -1 5 19 -1 -1 -1 5 10 -1 -1 16 25 8 24 -1 5 8 14 -1 21 22 5 20 -1 29 20 6 -1 11 20 9 17 -1 -1 28 -1 -1 -1

    The original reads:
    >1_10_531_F3
    T.11011..010..31...20..300..301.00.0.30...200..0...
    >1_10_536_F3
    T.01300.3100..00...12..0000.000.0030.010.0300..0...
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