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

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

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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
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5
oracleIndexTblSpc=NONE