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  • Euler 2.0

    I've tried to use EULER 2.0 to do the de novo assembly process.
    However, there are error messages:
    sh: line 1: 20961 Segmentation fault /home/echo/denovo/euler2_linux/trans_qual -i test.fasta -o test.fasta.reads -H >> test.fasta.log
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.txt': No such file or directory
    mv: cannot stat `reads.txt.score': No such file or directory
    mv: cannot stat `reads.aln': No such file or directory
    rm: cannot remove `G_*.gvz': No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_et: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_db: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory


    I have no idea why the messages would appear.
    Does anybody know the reason and how could I solve the problem?
    Thanks a lot.

  • #2
    Originally posted by ECHo View Post
    I've tried to use EULER 2.0 to do the de novo assembly process.
    However, there are error messages:
    sh: line 1: 20961 Segmentation fault /home/echo/denovo/euler2_linux/trans_qual -i test.fasta -o test.fasta.reads -H >> test.fasta.log
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.tmp': No such file or directory
    mv: cannot stat `reads.tmp.score': No such file or directory
    mv: cannot stat `reads.txt': No such file or directory
    mv: cannot stat `reads.txt.score': No such file or directory
    mv: cannot stat `reads.aln': No such file or directory
    rm: cannot remove `G_*.gvz': No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_et: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_db: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
    sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory


    I have no idea why the messages would appear.
    Does anybody know the reason and how could I solve the problem?
    Thanks a lot.
    "A segmentation fault (often shortened to segfault) or bus error is generally an attempt to access memory that the CPU cannot physically address."

    --Wikipedia

    It means that there is at least one programming error in the source code of EULER 2.0.

    The usual way to fix that is to

    1. Run the code inside gdb
    2. Locate the bug and fix it
    3. ???
    4. Profit.

    For your information, you are not alone: euler-sr problems [http://seqanswers.com]

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