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OrthomclLoadBlast: I am not getting the log file or SimilarSequences table.

I am running orthomcl for 6 species to find orthologs. I used the orthomclLoadBlast command to load the blast result. However, I am not getting any output file even after running the command successfully without any errors. Any suggestion or feedback will be highly appreciated. Thank you!

mysql orthomcl
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updated by GenoMax GenoMax • written by vasundharak • vasundharak

My suggestion is to use something other than OrthoMCL - I'm quite happy with orthofinder. OrthoMCL is ok but it's clunky and it hasn't been update for years. However, if you want an answer to your post you need to give more information.

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written by dariober dariober

Thank you for your suggestion. Could you tell me what information would help?

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written by vasundharak • vasundharak

orthomclLoadBlast /etc/orthomcl.config similarSequences.txt- this is the command is have used.

And this is my configuration file.

dbVendor=mysql
dbConnectString=dbi:mysql:orthomcl:mysql_local_infile=1
dbLogin=orthomcl
dbPassword=passwd
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5
oracleIndexTblSpc=NONE
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updated by GenoMax GenoMax • written by vasundharak • vasundharak

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