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  • #1

    ABYSS pe error

    Hello, I got this error message from ABYSS -pe

    error: removing `contigs-0.fa': No such file or directory

    What should I do to make it works?

    Thank you.
    Tags: None
  • #2
    Give us more information on how you are running ABySS. This is not a common error.

    Comment

    • #3
      This is the command that I used:

      /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'



      This is how the end of the logfile looks like:


      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      0: Assembled 355161061 k-mer in 7443983 contigs.
      Assembled 355161061 k-mer in 7443983 contigs.
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-1.fa
      Concatenating fasta files to testtest-bubbles.fa
      Done.
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory
      error: removing `contigs-0.fa': No such file or directory

      ===================================================================================
      = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
      = PID 62249 RUNNING AT gntcs-alit-hp1
      = EXIT CODE: 9
      = CLEANING UP REMAINING PROCESSES
      = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
      ===================================================================================
      YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
      This typically refers to a problem with your application.
      Please see the FAQ page for debugging suggestions
      make: *** [testtest-1.fa] Error 15
      -bash-4.1$

      Comment

      • #4
        This is the command I used:

        /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hise/abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'q/PE2P.fastq'


        This is the tail of the logfile:
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-1.fa
        0: Assembled 355161061 k-mer in 7443983 contigs.
        Assembled 355161061 k-mer in 7443983 contigs.
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-1.fa
        Concatenating fasta files to testtest-bubbles.fa
        Done.
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory
        error: removing `contigs-0.fa': No such file or directory

        ===================================================================================
        = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
        = PID 62249 RUNNING AT gntcs-alit-hp1
        = EXIT CODE: 9
        = CLEANING UP REMAINING PROCESSES
        = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
        ===================================================================================
        YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
        This typically refers to a problem with your application.
        Please see the FAQ page for debugging suggestions
        make: *** [testtest-1.fa] Error 15
        -bash-4.1$

        Comment

        • #5
          I ran it remotely using this command

          /abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hise/abyss-pe np=50 name=testtest k=45 in='./Hiseq/PE1P.fastq ./Hiseq/PE2P.fastq'q/PE2P.fastq'

          This is the tail of the log file

          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-1.fa
          0: Assembled 355161061 k-mer in 7443983 contigs.
          Assembled 355161061 k-mer in 7443983 contigs.
          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-1.fa
          Concatenating fasta files to testtest-bubbles.fa
          Done.
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory
          error: removing `contigs-0.fa': No such file or directory

          ===================================================================================
          = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
          = PID 62249 RUNNING AT gntcs-alit-hp1
          = EXIT CODE: 9
          = CLEANING UP REMAINING PROCESSES
          = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
          ===================================================================================
          YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
          This typically refers to a problem with your application.
          Please see the FAQ page for debugging suggestions
          make: *** [testtest-1.fa] Error 15
          -bash-4.1$

          Comment

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