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Old 07-05-2016, 07:44 AM   #1
asapp
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Location: Cambridge, MA

Join Date: Jun 2015
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Default 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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Old 07-05-2016, 08:13 AM   #2
asapp
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Old 11-01-2018, 06:45 PM   #3
Sin Lee
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Location: Guangzhou, China

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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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bioinformatics, genomics, ortholog, orthomcl

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