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asapp 07-05-2016 06:44 AM

OrthoMCL Pairs no output

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?


asapp 07-05-2016 07:13 AM

Question resolved

Sin Lee 11-01-2018 05:45 PM

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.

Sin Lee

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