Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

    Latest Articles

    Collapse

    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM
    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    59 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    57 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    56 views
    0 likes
    Last Post seqadmin  
    Working...
    X