Question: orthomclInstallSchema issue in OrthoMCL program
0
gravatar for wangdp123
3.0 years ago by
wangdp123240
Oxford
wangdp123240 wrote:

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

orthomcl • 1.3k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by wangdp123240
1

You may try this tutorial.

ADD REPLYlink written 3.0 years ago by h.mon29k

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.

ADD REPLYlink written 3.0 years ago by Joe16k
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