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  • mines
    Junior Member
    • Nov 2016
    • 4

    #1

    SOAP denovo permission denied

    Hi!
    I'm new to bioinformatics and linux.
    I've downloaded the latest pre-compiled binary version of SOAPdenovo2 and placed it in a directory in my Desktop. I unpacked it using tar -zxf.
    I also created a config file and have all my fastq, fasta and bam files ready on another directory in my Desktop.

    My issue is that when I change directory to /bin and type the command:
    /path/SOAPdenovo-63mer all -s /path/config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err
    I get
    Bash: ass.log permission denied

    I already tried chmod 777 to SOAPdenovo-63mer and to ass.log so that they have all the permissions and even added from /etc with sudo nano /etc/sudoers the user to execute with admin permission evethough there's only one user and is the admin.

    What should I do?
    Thanks!!
    Last edited by mines; 11-22-2016, 06:57 PM.
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    You don't want to write data files to the SOAPdenovo/bin directory. You can add a path to /some_path/ass.log and /some_path/ass.err files so they are saved somewhere else other than the SOAP dir hierarchy.

    Comment

    • mines
      Junior Member
      • Nov 2016
      • 4

      #3
      Hi GenoMax, thanks a lot for your answer.

      I don't have any SOAPdenovo directory in /bin, i just go there to execute it, should I do something about that?

      The ass.log and ass.err files are automatically created in the SOAPdenovo directory in my desktop where I have the SOAPdenovo-63mer file.
      The ass.err file says SOAPdenovo-63mer command not found.

      Thanks again!

      Comment

      • mines
        Junior Member
        • Nov 2016
        • 4

        #4
        Sorry, I meant bam files instead of bin when I wrote fastq, fasta and bin files ready.

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142

          #5
          You don't need to go to /bin directory to execute other programs (e.g. SOAP). You may want to spend a bit of time understanding basics of UNIX to clarify this. Follow this guide.

          Comment

          • mines
            Junior Member
            • Nov 2016
            • 4

            #6
            I definitely will. Thanks for the guide GenoMax!

            Comment

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