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OrthoMCL Pairs no output

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  • Sin Lee
    replied
    Hi, asapp

    I met the same problem that orthomclPairs finishes immediately with no output or error information. I'll appreciate it if you can share your solutions.

    Thanks,
    Sin Lee

    Leave a comment:


  • asapp
    replied
    Question resolved

    Leave a comment:


  • asapp
    started a topic OrthoMCL Pairs no output

    OrthoMCL Pairs no output

    Hello,

    I'm trying to run the OrthoMCL pipeline and haven't had any issue until the OrthoMCL Pairs step. I have a SimilarSequences table in my MySQL database, a config file that correctly specifies everything, and I've checked the SimilarSequences table to make sure all the data is present as it should be. However, when I run the program with: orthomclPairs orthomcl.config pairs.log cleanup=only, the program 'finishes' immediately with the log file saying 'Done' and nothing else (no data in the ortholog table, etc). Any idea how I could have gone wrong?

    Thanks!
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