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  • 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!

  • #2
    Question resolved

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    • #3
      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

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