Orthomclpairs Doesnt Work

Question

[User 4041]

Hello everyone,

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

..skipping'coOrthologsNormalization'...
Done

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

Thank you

[tanvi.phaltane]

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?

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Config_file:

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

Answer 1

[arnstrm]

If you use cleanup=no then all intermediate files will be saved. This will let you to restart orthomclPairs from the failed step onwards. So, after you run orthomclPairs, check the orthomcl.log file, If it says Done! at the end, that means the program finished successfully. If not, you can re-run the analyses from the step that finished successfully. For eg., orthomclPairs orthomcl.config orthomcl.log startAfter=inParalogTaxonAvg will re-run pairs program from inParalogTaxonAvg step onwards.