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  • Maq: Segmentation Fault

    Hi

    I am trying to map my SOLiD reads in Maq. I have converted my reads from .csfasta and .qual to .fastq using 'solid2fastq.pl'. I then generated a binary file using 'maq fastq2bfq'. I turned my reference genome (GRCh37) from .fa to .csfa using 'maq fasta2csfa' and made this binary using 'fasta2bfa'.

    When I use 'maq map' I get a segmentation fault. There is no other information. Here is my command;

    maq map -c aln.cs.map ref.csbfa reads.bfq 2> aln.log

    Does anyone have any ideas what could be causing this? I am currently using v0.7.1, but have tried the same command on earlier versions and get the same. I am wondering is the 'maq fasta2csfa' accepts reference in '.fa'?

  • #2
    I have recently experienced a similar problem. I am also attempting to use MAQ to map my SOLiD reads.

    I had recieved the .fastq files from a collaborator so I first used "maq fastq2bfq" and "maq fasta2csfa" and then ran the following the command:

    maq map -c out.cs.map ref.csbfa reads_1.bfq reads_2.bfq 2

    I got back the following error:

    -- maq-0.7.1
    [ma_load_reads] loading reads...
    [ma_load_reads] set length of the first read as 1.
    [ma_load_reads] set length of the second read as 1.
    maq: read.cc:61: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strncmp(name, lr->name[j], tl-1) == 0' failed.

    I then tried to go back a step and use the .csfasta and _QV.qual files to create the .fastq files using solid2fastq.pl. This ran with no error, howvever, the output files are empty!

    I am stuck. Can anyone offer any advice??

    Sincere thanks,

    Tench

    Comment


    • #3
      @TenchBB: Please do not double-post in two different forums (or here for that matter). Thank-you!

      Comment

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