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  • Asking help for installation of SOAPdenovo

    Hello, guys, I am completely new in Linux Operation System and genomics software.
    Recently I am learning to use SOAPdenovo. I had downloaded the latest version of SOAPdenovo (1.05), and unpacked it, and also type"make" and "make install" to install it.
    After that, I was also prepared the config file.
    then, I just type "./SOAPdenvo"
    computer says: "

    Usage: SOAPdenovo <command> [option]
    pregraph construction kmer-graph
    contig eliminate errors and output contigs
    map map reads to contigs
    scaff scaffolding
    all doing all the above in turn

    then, I type "./soapdenovo all -s config_file -o output_prefix"
    but the computer only says: "bash: ./soapdenovo: No such file or directory"

    therefore, I had tried all that I can, but the software just cannot run properly. So Please tell me how to get it started properly!

    Just thanks so much for help!
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  • #2
    Linux commands and filenames are case sensitive. The command is "SOAPdenovo" not "soapdenovo".

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    • #3
      Hey! I am experiencing the similar problem but in the following step. When I put

      ${bin} all -s config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err
      # I put my path and my config file

      the terminal says

      ${bin} all -s config_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

      what does it mean and how to sove it?

      Thanks!

      Comment

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