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  • Repeat masker installation

    Hi

    I downloaded repeat masker and ran the configure file. However if I now locate that directory in terminal and then use the command 'RepeatMasker' it says:

    RepeatMasker: command not found

    I have also tried 'repeatmasker'

    What might cause this to happen. Could it be something to do with the other prerequisites or is there a particular place where I must place the RepeatMasker directory?

    I'm not sure which information you need to help me. I could be that I've simply not installed it properly but I did follow the instructions and I'm not sure what else I can do! Hope you can help

    Thanks

    Jon

  • #2
    You probably need to make the file executable.

    Do you see the file with a long listing such as "ls -l"? If you do then you can do:
    Code:
    chmod u+x RepeatMasker
    Then you should be able to run the program by doing:
    Code:
    ./RepeatMasker -help

    Comment


    • #3
      That's great thanks! Worked perfectly. I can now run the RepeatMasker command. Unfortunately, however, I now have a new problem. I typed the command:

      Code:
      RepeatMasker -species petunia petunia.fa
      It gets to the point where it says 'analysing petunia.fa' and stays there for a while until eventually the message 'killed' is displayed and the process stops. Do you have any idea why this might be?

      Am I missing some parameters? I know I might ultimately have to tweak the defaults to get the results I need but just as a test I thought this command had the basics required to at least produce something.

      Thanks again
      Last edited by jomaco; 10-22-2011, 02:33 AM.

      Comment


      • #4
        prompt>RepeatMasker -help (or the RepeatMasker command issued in its own) should print a help message out with possible command line options. See if you are missing an option.

        You may also need to redirect the output to a file such as:

        Code:
        RepeatMasker -species petunia petunia.fa > output.fa
        PS: I do not have RepeatMasker installed to test. Perhaps tomorrow.

        Comment


        • #5
          Thanks for your help again but I couldn't see that I missed anything. I tried the '>' idea too but no luck. I tried to configure the program again and when this didn't work I thought it might a good idea to re-download everything and start from scratch. Same problem though - it stills just runs for a while, displaying nothing, until it says 'killed'

          Comment


          • #6
            I had the killed problem a couple of times two. It appears often, when your out of working memory. RepeatMasker needs a lot of RAM when you try to mask a whole genome.

            Comment


            • #7
              Hi. 'petunia.fa' is the whole petunia genome and is a 1.3GB file. When you a say a lot of memory, how much do you mean? I am trying this on a PC running ubuntu with 4GB RAM. Would it be useful to try it with a different UNIX based OS or do I need a better spec system?

              Thanks

              Comment


              • #8
                Just watch your run in another terminal with 'top' and see how much memory it consumes. If it is a memory problem (which it probably is) then you need to move to a machine with more memory.

                Comment


                • #9
                  I agree with sklages. Just check, how much memory is consumed. I work with a 8 GB Station and was unable to mask the Human Genome with all its species specific repeats, but for example masking the pig with this options was OK. But not only the size of the genome file is important. The number of repeats in the lib you are using is important for the needed working space too. So you could try to separate your your lib or your Genome and run only the parts with the RepeatMasker and compile the results.

                  Comment


                  • #10
                    It was indeed a memory problem. Top showed that memory usage climbed up to 80% with 100% CPU usage. I accessed /var/log/kern.log which reported '...ubuntu kernel: [19459.333979] Out of memory: Kill process 4677 (RepeatMasker) score 646 or sacrifice child'.

                    I will be switching to a computer with much more memory when possible. Thanks for all your help.

                    Comment

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