I have done the orthomclLoadBlast step before the orthomclPairs successfully and obtained a SimilarSequences table in the orthomcl database that I created. The SimilarSequences table has the blast results as expected. However when using the following command
home/username/bin/orthomclSoftware-v2.0.2/bin/orthomclPairs orthomcl.config orthomcl.log2 cleanup=yes
the last two lines of the orthomcl.log2 file were
and the Ortholog, InParalog, coOrtholog tables in the orthomcl database are still empty
P.S. The config file has the name of the SimilarSequences it will use written correctly
I would appreciate any suggestions about what I can do to know where the mistake was done. I am not sure if it is in the command line I have written or in the database tables that were created
Hi ! I am using orthomcl to identify orthologs, paralogs and co-orthologs between a fungus (Cochliobolus sativus) and model organism (S.cerevisiae, A.thaliana). All is well till orthomclPairs step, but when I run orthomclPairs script, the logfile shows no error but the final tables (CoOrtholog, InParalog, Ortholog) are empty. Can anyone point out what might be the reason for this?
dbVendor=mysql dbConnectString=dbi:mysql:orthomcl_sce:localhost:3307 dbLogin=root dbPassword=root similarSequencesTable=SimilarSequences orthologTable=Ortholog inParalogTable=InParalog coOrthologTable=CoOrtholog interTaxonMatchView=InterTaxonMatch percentMatchCutoff=50 evalueExponentCutoff=-5 oracleIndexTblSpc=NONE