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  • BabyFaruda
    Member
    • May 2014
    • 11
    #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
    • westerman
      Rick Westerman
      • Jun 2008
      • 1104
      #2
      Give us more information on how you are running ABySS. This is not a common error.

        Comment

        • BabyFaruda
          Member
          • May 2014
          • 11
          #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

            • BabyFaruda
              Member
              • May 2014
              • 11
              #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

                • BabyFaruda
                  Member
                  • May 2014
                  • 11
                  #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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