orthomclInstallSchema issue in OrthoMCL program

Question

[wangdp123]

Hi there,

I have been struggling with the analysis of data on OrthoMCL program and it always come up with the issue as follows when the analysis arrive at the "orthomclInstallSchema" step. In addition, I have confirmed that DBI and DBD::mysql have been installed already.

The command line is:

orthomclInstallSchema orthomcl.config install_schema.log

The reported error is:

DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (22) at ../lib/perl/OrthoMCLEngine/Main/Base.pm line 56

The content in orthomcl.config:

dbVendor=mysql
dbConnectString=dbi:mysql:orthomcl:3307
dbLogin=orthomcl
dbPassword=XXXXXXX
similarSequencesTable=SimilarSequences 
orthologTable=Ortholog
inParalogTable=InParalog 
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch 
percentMatchCutoff=50
evalueExponentCutoff=-5 
oracleIndexTblSpc=NONE

Any solution to get around this?

Many thanks,

Regards,

Tom

[h.mon]

You may try this tutorial.

[Joe]

This doesn't solve your problem as such, but frankly OrthoMCL is crazy difficult to use in my opinion. Assuming you're trying to define a core/pan-genome etc. Roary can do everything OrthoMCL does in a matter of minutes. Strongly recommended.