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  • SOAPdenovo command not found error (linux)

    Hi Everyone !
    I'm new to this field of genome sequencing and generating contigs.
    I've downloaded the latest bin version of SOAPdenovo2 and placed it in a directory in my Desktop.
    I've also edited my config file to match my parameters and path to my data set.
    My issue is that when I go to the terminal and type the command:

    SOAPdenovo-63mer
    or

    SOAPdenovo-63mer all -s metasim_config -K 63 -p 1 -o jack>log
    I get this error:

    SOAPdenovo-63mer: command not found
    I've checked the permissions (and I'm the admin anyway), and the SOAPdenovo-63mer is located in the same directory where I am, and I've looked at it's properties and it does say its an executable file.

    So, what am I missing here ?

  • #2
    SOAPdenovo-63mer file should be in a directory in your PATH environment.
    you can export the PATH to your SOAPdenovo-63mer file by adding the path of the directory to the path environment

    Use:
    export PATH=$PATH:/path/to/the/soapdenovo/directory

    (of course this will work only in the terminal your export the path and have to do every time you open a new terminal. to avoid this you can place the SOAPdenovo-63mer in any folder accessed by PATH or change the .bashrc file)

    or place the SOAPdenovo-63mer in the directory from where you are executing it and use

    ./SOAPdenovo-63mer

    Comment


    • #3
      Great ! Works like a charm !
      Thanks!

      Comment


      • #4
        Hey! I am having the same problem. How do you find the path for SOAPdenovo? (im using Linux)

        Comment


        • #5
          Originally posted by BabyFaruda View Post
          Hey! I am having the same problem. How do you find the path for SOAPdenovo? (im using Linux)
          Did you compile the software/do the install (or someone else did)?

          Comment


          • #6
            someone did it for me. I think she did the "make".

            Comment


            • #7
              This is probably not going to work but can you first try

              Code:
              $ which SOAPdenovo-63mer
              If you are new to unix (command line) then it may be a good investment to read through this for some UNIX basics. http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

              If you are the impatient kind try to see if the command below can locate the program

              Code:
              $ find ~ -name "SOAPdenovo-63mer" -print
              If that does not produce anything then try (could take some time):

              Code:
              $ find / -name "SOAPdenovo-63mer" -print

              Comment


              • #8
                thanks! I got the path from the first code you gave.

                Comment


                • #9
                  I am experiencing another problem.

                  I am now working in just 1 path. The SOAPdenovo, the configuration file, and the sequence data are in the same directory.

                  The command I used is

                  all -s file.config -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

                  I got 2 files for the output: the log file (emtpty) and the err file which says

                  No command 'all' found, did you mean:
                  Command 'al2' from package 'mono-devel' (main)
                  Command 'alc' from package 'amule-utils-gui' (universe)
                  Command 'alc' from package 'amule-adunanza-utils-gui' (universe)
                  Command 'als' from package 'atool' (universe)
                  Command 'ali' from package 'mailutils-mh' (universe)
                  Command 'ali' from package 'nmh' (universe)
                  Command 'al' from package 'mono-devel' (main)
                  Command 'axl' from package 'afnix' (universe)
                  Command 'wall' from package 'bsdutils' (main)
                  Command 'ale' from package 'ale' (universe)

                  What should I do?

                  Comment


                  • #10
                    I think you need to do

                    Code:
                    $ SOAPdenovo-63mer all -s file.config -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

                    Comment


                    • #11
                      Hi!
                      I use soapdenovo1.04 and type the command:

                      ./SOAPdenovo pregraph -s a.config -K 31 -d 1 -o test>test.log

                      after that I only got :test.log
                      test.edge
                      test.kmerFreq
                      these 3 files ,without the test.preGraphBasic file. And I cannot go to the next step. Can someone help me ?

                      Comment

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