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  • MAQ - Segmentation fault

    Hi all,

    I just started with the DNA sequencing and analysis area and everything is all new to me. So please be easy on me.

    Now I am trying to learn how to align and analyze data. I downloaded MAQ, compiled it (in PowerPC G5 computer), copied maq, maq.pl etc to runfiles director, and try to run with a test data file as suggested in MAQ

    Code:
    maq.pl demo ref.fasta calib-36.dat
    Calib-36.dat came together with the MAQ package, and ref.fasta is as simple as

    Code:
    >D86934(D86934)probable sugar-nucleotide dehydratase [imported] - Mycobacterium leprae
    MYGEPVRALVTGAAGFIGSTLVDRLLADGHTVVGLDNFATGHAANLEHLASTPALAFVEA
    DIVTADLQTILDEHRPEVVFHLAAQIDVRHSVVDPQFDASVNVIGTVRLAEAARHTGVRK
    IVHTSSGGSIYGTPSQYPTPETVPTDPTSPYAAGKVAGEIYLNTFRHLCGLDCSHIAPAN
    VYGPRQDPYGEAGVVAIFVQALLSDRPTKVFGDGTHTRDYVFVDDVVDAFIKASGDAGGG
    QRFNIGTGIETSDRQLHTAVSAAVGGPDDPEFHPPRLGDLKRSCLDIGLATTVLGWSPQV
    QLDDGVRRTVEYFRAAQRS
    After a while, I got Segmentation fault error:

    Code:
    -- CMD: mkdir -p maqdemo
    -- CMD: /usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp
    -- 1 sequences, total length: 319
    sh: line 1: 37110 Segmentation fault      /usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp
    ** fail to run command '/usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp' at /usr/local/bin/maq.pl line 842.
    What I am doing wrong, or is this any missing step that I forget? Anybody help please!
    Last edited by dukevn; 04-29-2009, 07:56 AM. Reason: fixed codes

  • #2
    Originally posted by dukevn View Post
    Hi all,

    Code:
    >D86934(D86934)probable sugar-nucleotide dehydratase [imported] - Mycobacterium leprae
    MYGEPVRALVTGAAGFIGSTLVDRLLADGHTVVGLDNFATGHAANLEHLASTPALAFVEA
    DIVTADLQTILDEHRPEVVFHLAAQIDVRHSVVDPQFDASVNVIGTVRLAEAARHTGVRK
    IVHTSSGGSIYGTPSQYPTPETVPTDPTSPYAAGKVAGEIYLNTFRHLCGLDCSHIAPAN
    VYGPRQDPYGEAGVVAIFVQALLSDRPTKVFGDGTHTRDYVFVDDVVDAFIKASGDAGGG
    QRFNIGTGIETSDRQLHTAVSAAVGGPDDPEFHPPRLGDLKRSCLDIGLATTVLGWSPQV
    QLDDGVRRTVEYFRAAQRS

    That doesn't look any DNA I have seen before!

    Comment

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